Cyclina sinensis and Anadara broughtonii are economically important bottom-sowing farming shellfish in China. Understanding their food sources can help quantify the interaction between shellfish and shallow sea aquaculture ecosystems and provide data support for the construction and screening of suitable bottom-sowing shellfish varieties for shallow sea comprehensive aquaculture models. In the present study, stable isotope and high-throughput sequencing technologies were used to determine the food composition characteristics of C. sinensis and A. broughtonii cultured in bottom sowings, and the differences and influencing factors of the food sources of the two shellfish were analyzed. Samples were collected from the bivalve culture area (BA) and bivalve kelp polyculture area (BKA) in Sanggou Bay in September 2021. The results showed the following: (1) The food sources of C. sinensis and A. broughtonii include phytoplankton, zooplankton, kelp detritus, shellfish biodeposition, seagrass detritus, C₄ plants, and terrestrial sediments. Among them, phytoplankton were the main food source of C. sinensis and A. broughtonii (accounting for 40.4%–79.6%). Zooplankton are the second food source and the contribution rate of zooplankton to A. broughtonii (35.6%–37.3%) was significantly higher than that of C. sinensis (13.3%–15.9%). There were regional differences in the contribution rates of shellfish biodeposition and kelp detritus to the food of C. sinensis and A. broughtonii. The contribution rates of shellfish biodeposition to C. sinensis and A. broughtonii in the BA were 2.0% and 7.4%, respectively. The contributions of shellfish biodeposition to C. sinensis and A. broughtonii in the BKA were 5.1% and 4.3%, respectively. The contribution rates of kelp detritus to C. sinensis and A. broughtonii in BA were 0.7% and 2.9%, respectively, and those to C. sinensis and A. broughtonii in BKA were 3.4% and 2.1%, respectively. (2) The main component in the stomach contents of C. sinensis was chlorophyta (the proportion reached 56.55%), followed by streptophyta (44.35%); the main component in the stomach contents of A. broughtonii was chlorophyta (47.27%), followed by chordata (30.3%). This was closely related to the feeding mechanisms of the two shellfish species and their physiological structures. The feeding mechanism of filter-feeding shellfish includes active and passive mechanisms, both of which are related to feeding organs. However, C. sinensis have water pipes that extend their feet and pipes before they are exposed, relying on the inlet and outlet pipes for feeding and excretion. A. broughtonii does not have water pipes and is selectively fed through gill filaments. There were also differences in the gill structures of the two shellfish. Different physiological structures lead to differences in feeding behavior between two shellfish species in the same culture area. The eukaryotic composition of the stomach contents of the two shellfish species was predominantly phytoplankton and came mainly from the bottom seawater; this was in agreement with the stable isotope results. (3) In BA and BKA, the contribution of organic matter (biodeposition and kelp detritus) produced by the raft culture to A. broughtonii was higher than that to C. sinensis. The contribution of kelp detritus to C. sinensis in BA was higher than that to A. broughtonii. From the perspective of food source structure, both A. broughtonii and C. sinensis can be used as bottom-sown shellfish in the comprehensive aquaculture area of Sanggou Bay, and C. sinensis is more suitable for bottom sowing in areas with algal cultures.