Phytoplankton functional types (PFTs) shape marine food webs and biogeochemical cycles, yet their spatial, seasonal, and vertical variability in marginal seas remains poorly resolved, largely because observations have been sparse and surface-limited. Here we characterize the depth-resolved community structure of nine pigment-based PFTs across the China Seas using a 4 km monthly reconstruction spanning 2002 to 2023. The reconstruction integrates HPLC-CHEMTAX observations from 87 cruises with multi-source environmental predictors through spatially validated LightGBM models, and resolves PFT concentrations at seven depths in the upper water column, each accompanied by uncertainty estimates and applicability-domain flags. The resulting fields capture major cross-shelf gradients, distinct seasonal succession, and pronounced vertical structure in community composition. By extending beyond surface-based products, they expose subsurface variability and depth-specific shifts in phytoplankton size structure that are invisible to satellite views alone. Together, these results demonstrate how high-resolution, depth-resolved observations sharpen our picture of plankton community variability in the China Seas, providing an observation-constrained basis for studying ecosystem change and biogeochemical processes in marginal seas.