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A monthly survey of the feeding selectivity of <i>Ruditapes philippinarum</i> in the Yalu River Estuary in 2020–2021 was conducted using high-throughput sequencing identification and visual grading technology. The results showed that the most-dominant species in the water of the shellfish culture area and in the stomachs of <i>R. philippinarum</i> was <i>Karlodinium veneficum</i> in those years. The selectivity index (E) indicated that <i>R. philippinarum</i> avoided consuming Bacillariophyta, Chrysophyta and Cryptophyta throughout the year and preferentially consumed Dinophyta and Chlorophyta. In 2020, the annual average biomass of Dinophyta, Bacillariophyta, Chlorophyta, Dictyochophyta, Cryptophyta and Chrysophyta in the stomach contents of <i>R. philippinarum</i> was 54:14:16:1:10:4; it was 41:12:28:0:1:17 in 2021. The annual average biomass ratio of picophytoplankton, nanophytoplankton and microphytoplankton in the stomachs of <i>R. philippinarum</i> was 13:48:39 in 2020; it was 14:66:20 in 2021. <i>R. philippinarum</i> actively fed on nanophytoplankton and avoided picophytoplankton. Among the phytoplankton of different sizes and groups that <i>R. philippinarum</i> prefer to feed, chemical oxygen demand (COD) and organic phosphorus (DOP) have a significant negative effect on the nanophytoplankton community, pH has a positive effect on the Dictyochophyta community and COD and the inorganic nitrogen to phosphorus ratio (DI-N/P) have a significant positive effect on the Chlorophyta community.