Understanding how individual body size influences the physiological metabolism and nutrient element budgets of bivalves is fundamental to elucidating their ecological roles in carbon (C), nitrogen (N), and phosphorus (P) cycling, as well as their potential contributions to coastal carbon sequestration. Bivalves, as dominant filter feeders in estuarine and coastal ecosystems, play a key role in regulating the flow of energy and nutrients within benthic food webs. The ark shell Scapharca subcrenata, an ecologically and economically important species widely distributed along the coasts of China, is a representative benthic organism that contributes substantially to biogeochemical cycling and sediment–water interactions. However, the influence of individual size variation on its elemental metabolism and nutrient allocation remains insufficiently understood. In this study, a series of controlled laboratory experiments were conducted to investigate how differences in individual size affect the respiratory metabolism and C, N, and P budgets of S. subcrenata. Three size classes of S. subcrenata were selected based on shell length—small (29.43 ± 0.88 mm), medium (36.42 ± 0.43 mm), and large (42.53 ± 0.59 mm)—and subjected to static-water experimental conditions. The experimental design ensured uniform environmental parameters such as temperature, salinity, and dissolved oxygen to minimize external influences. For each size group, the feeding rate, feces production rate, oxygen consumption rate, ammonia excretion rate, and phosphorus excretion rate were measured. Based on these parameters, comprehensive C, N, and P budget equations were constructed to quantify the absorption, utilization, and loss of nutrients, thereby providing an integrated assessment of how size variation influences the energy balance and nutrient utilization efficiency of this species. The results revealed that all measured metabolic indices decreased significantly with increasing body size (P < 0.05). Specifically, smaller individuals exhibited notably higher feeding rates, oxygen consumption rates, and excretion rates compared with medium- and large-sized individuals. This indicates that small-sized S. subcrenata are characterized by more active physiological metabolism and greater nutrient turnover, reflecting their higher energy demand during rapid tissue growth and organ differentiation. In contrast, larger individuals displayed lower metabolic activity, which is consistent with a physiological shift toward maintenance metabolism and metabolic homeostasis at later developmental stages. These results align with general patterns observed in bivalve physiology, where metabolic intensity tends to decrease with increasing body size. In terms of nutrient element allocation, significant differences were observed among size groups. The small-sized group devoted the highest proportion of assimilated carbon, nitrogen, and phosphorus to growth, accounting for 38.0%, 42.2%, and 37.0% of their respective total budgets. These proportions were significantly greater than those of the medium- and large-sized groups (P < 0.05), indicating that small individuals allocated more assimilated energy and nutrients toward biomass accumulation and structural growth. Conversely, large-sized individuals showed markedly higher proportions of assimilated carbon consumed through respiration (58.6%) and of nitrogen (59.5%) and phosphorus (23.7%) lost through excretion (P < 0.05). This pattern suggests that large individuals invest more resources into sustaining basic metabolic functions rather than new tissue synthesis. The calculated growth scopes for C, N, and P all exhibited a pronounced declining trend with increasing size. The growth scope of small-sized individuals was approximately 50% higher than that of large individuals, highlighting the superior nutrient conversion efficiency and growth potential of smaller S. subcrenata. As the organisms increased in size, their growth scopes decreased significantly, implying that physiological energy allocation gradually shifted from biosynthetic activity to metabolic maintenance. Such changes are consistent with ontogenetic metabolic scaling laws, wherein metabolic rate per unit body mass decreases as organisms grow larger due to reduced proportions of metabolically active tissues. These findings reveal distinct size-dependent strategies in the energy and nutrient allocation of S. subcrenata. Small individuals exhibit a “growth-oriented” strategy characterized by high assimilation efficiency, elevated metabolic rates, and active anabolism, which supports rapid somatic growth. In contrast, larger individuals demonstrate a “maintenance-oriented” strategy, in which energy and nutrient resources are primarily directed toward respiration and excretion to sustain physiological equilibrium. This ontogenetic shift from growth-dominated to maintenance-dominated metabolism underscores the species’ adaptive physiological plasticity and may influence its ecological functions across life stages. From an ecological perspective, these results provide new insights into how size structure regulates the elemental cycling of bivalve populations in coastal ecosystems. The differences in C, N, and P utilization among size classes suggest that populations dominated by smaller individuals contribute more effectively to carbon fixation and biomass accumulation, while populations with larger individuals play a greater role in nutrient regeneration through excretion. Consequently, variations in population size structure may directly influence the carbon sequestration potential and nutrient cycling efficiency of bivalve communities in aquaculture environments. Moreover, the establishment of detailed C, N, and P balance equations in this study offers a quantitative framework for evaluating the elemental metabolism of S. subcrenata. Such data provide critical references for assessing its role in benthic biogeochemical cycles and for predicting how environmental factors and aquaculture practices might alter its ecological functions. These insights have broader implications for the optimization of shellfish aquaculture systems, particularly in the context of developing low-impact, carbon-neutral mariculture models that integrate ecological efficiency with sustainable production. In summary, this study demonstrates that individual body size significantly affects the respiratory metabolism and nutrient budgets of S. subcrenata, resulting in distinct metabolic strategies across size groups. Smaller individuals exhibit higher nutrient utilization efficiency and stronger growth potential, while larger individuals shift toward metabolic maintenance and lower energy turnover. These findings contribute to a more comprehensive understanding of size-dependent metabolic regulation in bivalves and highlight the importance of size structure in determining their ecological roles in carbon, nitrogen, and phosphorus cycling. The results also provide a theoretical basis for evaluating the carbon storage potential of bivalve populations and for guiding future strategies in nutrient management and sustainable mariculture development.