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Understanding the diet composition and feeding habits of bivalve shellfish is crucial for developing conservation measures to enhance their resources. This is particularly important for the main economic species in shellfish-producing regions. In this study, we analyzed the stomach contents composition of the two main economic shellfish in Geligang, specifically Meretrix meretrix and Mactra veneriformis, using high-throughput sequencing. The results revealed that 956 operational taxonomic units (OTUs) were common to both M. meretrix and M. veneriformis, with 1117 OTUs unique to M. meretrix and 412 OTUs unique to M. veneriformis. We identified a total of 50 bait organisms from 11 phyla. The main taxa in the stomach contents of M. meretrix were Chlorophyta, Cryptophyta, Pyrrophyta and Bacillariophyta, while Cryptophyta, Chlorophyta, Pyrrophyta and Chrysophyta dominated the stomach contents of M. veneriformis. Non-metric multidimensional scaling (NMDS) analysis indicated less compositional variety in the stomach contents of M. meretrix compared to M. veneriformis. Additionally, the Linear Discriminant Analysis Effect Size (LEfSe) results showed a significant difference in food composition between the two species. Specifically, M. meretrix and M. veneriformis preferred feeding on Bacillariophyta, Chlorophyta, and Cryptophyta, while M. veneriformis favored Chrysophyta. Overall, our study provides fundamental insights for ecological research on feeding habits and resource conservation of M. meretrix and M. veneriformis in Geligang, which can inform the development of effective conservation measures for the shellfish resources.