Anthropogenic pressures have increasingly threatened lacustrine ecosystems in the Anthropocene. However, it remains unclear how classical biogeographical patterns in the biodiversity of lacustrine planktonic communities—such as the species-area relationship, elevation diversity theory, and distance-decay relationship—may have shifted, especially with respect to community group mean body size. In this study, we used a standardized environmental DNA (eDNA) metabarcoding approach to investigate the biodiversity of twelve co-occurring communities across the aquatic food webs at a continental scale in China, including free-living and particle-attached diazotrophs, bacteria, fungi, protists, algae, rotifers, cnidarians, arthropods, mollusks, and fish. Our research encompassed 230 lakes across China, covering a wide range of geographical, natural, and human-influenced conditions. The lakes varied significantly in longitude (74.99°E to 134.28°E), latitude (23.42°N to 49.87°N), elevation (-155 to 5010 m), pH (6.85 to 14.29), salinity (0.00 to 150.53 ppt), and trophic state index (4.28 to 105.22). Our results showed consistent biogeographic community structures and alpha and beta diversity patterns across these multi-trophic communities, despite large differences in group mean body size. We found that the environmental diversity gradient and distance decay patterns for different groups were positively correlated with group mean body size. Larger-bodied communities (at higher trophic levels) demonstrated significantly higher response rates to environmental changes and greater species spatial turnover rates compared to smaller-bodied plankton. Variation partitioning analysis revealed that the variance in each taxonomic community explained by natural, human, and geographical factors increased monotonically with group mean body size. This study is the first to profile holistic lacustrine planktonic communities at a continental scale, revealing a consistent biogeographic structure with a body-size-dependent response rate. Our findings advance ecological theory related to body-size dependent of biodiversity pattern and emphasize targeted conservation efforts are essential to address the differential impacts of environmental changes based on organism body size.