China is home to the most productive marine shellfish aquaculture industry, and aquaculture production has increased rapidly in recent decades. In 2023, production stood at 16,460,600 tons, with an aquaculture area of 1,357.53 thousand hectares. Marine shellfish farming in China has made important contribution to increasing fishermen's income, improving water transparency, alleviating water eutrophication, and actively responding to climate change. However, on the whole, the marine shellfish aquaculture industry in China is still a labor-intensive and volume-driven industry, and the improvement of aquaculture output is highly dependent on the expansion of the aquaculture area. In the past two decades, marine shellfish aquaculture in China has increased by 28.11% in terms of cultivation area and maintained a 54.19% increase in aquaculture output. With increasingly fierce competition for marine space resources from various marine industries such as coastal tourism and marine transportation, mariculture is increasingly constrained by space. In this context, it is urgent to seek scientific ways to improve the production efficiency in limited space. It is one of the effective ways to enable the industry to improve production efficiency. In many new aquatic varieties, the growth rate is usually one of the important target breeding traits. As the single highest yield of cultured shellfish in China, Ruditapes philippinarum is distributed in the major sea areas of China's north and south, with an annual output of more than 4 million tons, accounting for 90% of the world's total output. The main new varieties of breeding are Zebra clam, white zebra clam, and Zebra clam 2. A total of 600 individuals were selected from a wild population in Shihe, Dalian, Liaoning Province, and the results showed that the shell length and total wet weight of 12 months increased by 10.6% and 19.5%, respectively, after 4 successive generations of population selection with the aim of shell color and growth rate. At present, the research on the new R. philippinarum species Zebra clam 2 variety primarily focuses on the influence of external environmental stress on metabolism and physiology, the comparison of breeding mode, the juvenile sand diving behavior, and ammonia nitrogen tolerance, etc. There are no reports on the comparative analysis of dietary metabolism, physiology, and energy budget between the two. In order to clarify the differences in feeding metabolic physiological processes and energy distribution strategies between Zebra clam 2 and unselected group, three sizes (shell length 40–45 mm, 35–40 mm and 30–35 mm, respectively) of Zebra clam 2 and unselected group were chosen as experimental subjects in July 2023. In Sanggou Bay, Rongcheng City, Shandong Province, the metabolic and physiological processes of food intake between the two groups were studied by the field flow method. The energy budget equation was constructed based on basic physiological parameters such as water filtration rate, ammonia discharge rate, and oxygen consumption rate, and the differences in energy distribution modes were compared and analyzed. The experimental results showed that the filtration rate and assimilation efficiency of the three specifications of Zebra clam 2 were higher than those of the unselected group, but the differences were not significant (P＞0.05). The oxygen consumption rate of medium-sized Zebra clam 2 was significantly higher than that of the unselected group (P＜0.05), while that of small-sized Zebra clam 2 was significantly lower than that of the unselected group (P＜0.05). The ammonia excretion rate of the medium and small size Zebra clam 2 was significantly higher than that of the unselected group (P＜0.05). In terms of energy budget, compared with the unselected group, the intake energy of large, medium and small size Zebra clam 2 increased by 45.22%, 18.60% and 21.40%, the absorption energy increased by 54.90%, 18.60% and 29.67%, and the growth power increased by 57.65%, 17.43% and 31.79%, respectively. This indicates that Zebra clam 2 of the same size showed higher energy intake (filtration rate) and slightly higher absorption efficiency than the unselected group. Although the energy consumption (oxygen consumption and excretion energy) of Zebra clam 2 of the same size was slightly higher than that of the unselected group, the proportion was relatively small (＜10%), so Zebra clam 2 showed a higher growth power and led to a faster growth rate due to its higher energy intake. The results of this study provide basic data for further understanding of the physiological characteristics of Zebra clam 2 and for evaluating the breeding capacity of this new variety.