The continuous rise in the concentration of greenhouse gases, such as carbon dioxide, in the atmosphere is triggering a series of climate change issues on a global scale, including global warming, frequent occurrences of extreme weather events, and sea-level rise. This not only threatens the stability of natural ecosystems but also poses severe challenges to food security, water resource allocation, and economic development of human society. Hence, it has become a core environmental hotspot of common concern to governments, scientific research institutions, and the public worldwide. As the largest and most active carbon pool on Earth, the ocean plays an irreplaceable role in regulating the global carbon balance through its carbon cycle processes. According to the authoritative report of the Intergovernmental Panel on Climate Change (IPCC, 2019), the ocean can absorb approximately one - third of the carbon dioxide emitted into the atmosphere by human activities each year, which significantly reduces the accumulation rate of greenhouse gases in the atmosphere and serves as a "natural buffer" for maintaining the global carbon balance and the stability of the climate system. Marine fisheries, as one of the pillar industries of the marine economy, not only provide about 30% of animal protein sources for billions of people around the world, acting as a key link in ensuring food security and building a diversified food supply system, but their ecological value has also been increasingly valued. Existing studies have confirmed that fishery systems are not merely resource-utilization activities. Some fishery models also have the function of "carbon sink" — they fix carbon elements through the growth and metabolism of organisms themselves, store them in the form of biomass, or sequester them through sedimentation. They play a unique and positive role in mitigating climate change, and this "production-carbon sequestration" synergistic effect provides important support for the development of the blue carbon economy. In coastal ecosystems, bivalves are core groups in both natural and aquaculture ecosystems. Their physiological activities, such as filtration, metabolism, and biological sedimentation, have a profound impact on the biogeochemical cycle of carbon. Numerous studies have demonstrated that bivalves convert carbon from water into their own biomass by filtering organic particles, such as phytoplankton. At the same time, they promote the migration of carbon to sediments through excretion and residue decomposition, playing a key driving role in the migration and transformation process of carbon. Therefore, they have become an indispensable biological factor in marine carbon sink research. Studies on physiological energetics are the main method to analyze the interaction between shellfish and carbon. At present, extensive research has been conducted on multiple species such as Crassostrea gigas, Chlamys farreri, Ruditapes philippinarum, Mytilus edulis, Pteria penguin, and Paphia undulata. However, on the one hand, most research objects focus on temperate shellfish, while relatively few studies have been carried out on the physiological energetics and carbon budgets of tropical/subtropical shellfish. On the other hand, processes such as water sample treatment and sample determination are greatly affected by human factors, and the objectivity and scientificity of experimental data urgently need to be improved. Pinctada fucata martensii, also known as the Hepu pearl oyster, belongs to Mollusca, Lamellibranchia, Pteriomorphia, Pterioida, Pteriidae. It is an important mariculture bivalve in China and the main host oyster for marine pearl cultivation. At present, research on Pinctada fucata martensii mainly focuses on genetic breeding, molecular genetics, biomineralization mechanisms, and optimization of pearl quality. Relevant studies on physiological energetics have mainly concentrated on the effects of transportation stress, environmental factors, and extreme weather events on its physiological energetics, with no research on physiological energetics under in-situ flowing water conditions. In this study, Pinctada fucata martensii was selected as the research object. In May 2024, the filtration rate, assimilation efficiency, oxygen consumption rate, and ammonia excretion rate of Pinctada fucata martensii of three size classes(large: shell length 7.27±0.75 cm; medium: shell length 5.20±0.21 cm; small: shell length 4.46±0.30 cm)were measured at Wuzhizhou Island, Sanya, and equations for energy budget and carbon budget were established. Before the experiment, Pinctada fucata martensii were acclimated for 3 days. The experiment was conducted using a standardized measurement method that combined a controllable in-situ flowing water experimental system with measurement technologies of a portable particle counter (PAMAS) and a multi-channel real-time dissolved oxygen meter(PreSens). The results showed that the filtration rates per unit dry weight of the soft body of large, medium, and small-sized Pinctada fucata martensii were (1.75±0.44), (1.30±0.29), and (0.51±0.19) L/(h·g), respectively. The filtration rates per unit dry weight of the soft body of large and medium-sized individuals were significantly higher than that of small-sized individuals (P < 0.01). The oxygen consumption rates and ammonia excretion rates of Pinctada fucata martensii of different sizes decreased with the reduction in size, but the differences were not significant (P > 0.05). The ranges of assimilation efficiency and oxygen-nitrogen ratio were 48%–68% and 2.26–17.68, respectively. The energy allocation of Pinctada fucata martensii of the three sizes all showed that fecal energy accounted for the largest proportion (52.00%–64.00%), followed by growth energy (26.28%–39.06%), and excretory energy accounted for the smallest proportion (1.36%–1.60%). The carbon budget equations for large, medium, and small-sized Pinctada fucata martensii were 100Cc=13.94Pc+46.97Rc+7.27Uc+31.82Fc,100Cc=19.80Pc+23.76Rc+3.96Uc+52.48Fc,100Cc=3.92Pc+43.14Rc+5.88Uc+47.06Fc, respectively. The research findings provide data support for further understanding the energy and carbon allocation patterns of?Pinctada fucata martensii?in tropical marine areas and evaluating its carbon sequestration capacity.