Shellfish in mudflat constitutes a crucial component of mariculture in China, with annual output accounting for about one-third of shellfish breeding output. The Manila clam Ruditapes philippinarum is one of the main cultivar species of mudflat mollusks in China, with the characteristics of short cultivation cycle, strong adaptability, low investment, and high profitability. It is a suitable excellent cultivar for artificial high-density cultivation, with an annual output exceeding 3 million tons, accounting for more than 90% of the world's cultured production. It is one of China's traditional four major cultured mollusk species and is highly valued for its delicate taste, rich nutrition, and popularity among the general public. Currently, the domestic Manila clam aquaculture industry has formed a mainstream pattern of southern (Fujian Province) breeding and northern (Liaoning Province and Shandong Province) seedling rearing. In the entire cultivation process of the Manila clam, the intermediate cultivation (cultivating juveniles to suitable sizes for bottom seeding cultivation) is an important link connecting the two stages of factory-based seed production and bottom seeding cultivation. With the increasing demand for Manila clam in the market year by year, its cultivation scale has also expanded, making the intermediate cultivation stage particularly important. Currently, the southern Manila clam juvenile intermediate cultivation stage is mainly carried out in natural sea areas, while the northern Manila clam is mainly reared in ponds for intermediate cultivation. Pond intermediate cultivation can be artificially controlled and managed, and juveniles are less affected by predators, making them easier to harvest. However, the disadvantage of northern pond intermediate cultivation lies in the problems of low temperature in winter and lack of food. However, the intermediate cultivation of juvenile shellfish is one of the key factors restricting the development of the industry. Studies have shown that the accumulation of nutrients in juvenile shellfish plays a decisive role in the survival rate of increased breeding, and more and more attention has been paid to it by breeding enterprises and researchers of these, ensuring the feed supply during the intermediate cultivation stage of Manila clam juveniles is crucial to the entire cultivation process. Therefore, this study aims to select effective or alternative microalgal feed supplements by adding nutritionally rich and easily obtainable spirulina powder, yeast, plasma protein powder, and soybean peptide. Soybean peptides represent a high-protein source that is obtained by harnessing biological enzymatic technology to break down large soybean protein molecules into smaller molecular fragments. This process yields a rich array of amino acids, making soybean peptides not only a concentrated source of protein but also a potentially beneficial component for enhancing the growth and immune function of mollusks in aquaculture. Plasma is the liquid part of blood and contains various proteins, minerals, hormones, and a spectrum of essential nutrients. It can be made into plasma protein powder in the aquaculture field and used as a protein supplement, which may provide essential nutrients for mollusks. Yeast is a microbial protein source that contains rich nutrients, including proteins, B-vitamins, minerals, and dietary fiber, which can be used as a nutritional supplement to help provide essential nutrients and may help improve the nutritional value and growth performance of young Manila clam. Spirulina is a high-quality plant-based protein source that contains rich proteins, vitamins, minerals, and essential amino acids, which may have a significant impact on the fat content, immunity enhancement, etc. of Manila clam in order to solve the problems of feed shortage or nutritional deficiencies. In this study, we employed experimental physiological ecology to investigate the effects of soybean peptide, plasma protein powder, yeast and spirulina powder on the growth, survival and nutrient accumulation of R. philippinarum juveniles. Specifically, we compared two substrate conditions (with and without sand) across four supplemental nutrient groups: H1 (soybean peptide), H2 (plasma protein powder), H3 (yeast), and H4 (spirulina powder). A control group, which received no nutrients was fed solely on microalgae, was also included. The results showed that the survival rate among the juveniles in the H3 group, which received yeast supplementation and were cultivated on a sandy substrate, was notably higher at 79.6%, demonstrating a significant difference when compared to those without sandy substrate (P<0.05). On the tenth day of observation, the maximum shell length specific growth rate of 1.09%/d was observed in the H4 group with sand, whereas the maximum wet weight specific growth rate of 3.11%/d was seen in the H3 group with sand. and the effect of substratum on growth rate was significant (P<0.05). Furthermore, the glycogen content of R. philippinarum juveniles in the H4 group with sand (67.89±0.52mg/g) was significantly higher than that in all other groups (P<0.05), and this difference between the groups with and without sand was also statistically significant (P<0.05). The carbon content of R. philippinarum juveniles in the H3 group with sand (45.23±0.33%) was significantly higher than that in the other groups (P<0.05). Similarly, the nitrogen content of R. philippinarum juveniles in the H4 group with sand (12.14±0.25%) was significantly elevated compared to the other groups (P<0.05). However, the difference in carbon content between the groups with and without substratum was not significant (P>0.05), while the difference in nitrogen content was significant (P<0.05). In conclusion, our study demonstrates that nutrient supplementation can significantly alter the nutrient content of R. philippinarum juveniles, and the change is partially influenced by the presence or absence of sand. The results of this study provided valuable insights and guidance for the cultivation of healthy R. philippinarum juveniles.