The composition of phytoplankton communities is critical for marine ecosystem stability and resilience. Anthropogenic activity has resulted in interdecadal succession in the phytoplankton community in the Bohai Sea (BS) over the last four decades, affecting ecosystem service functions and producing a variety of ecosystem health issues. We integrated the past five years’ findings on diatom-dinoflagellate succession, developed and validated an efficient Nutrients-Diatom/Dinoflagellate-Detritus (N-Dia/Dino-D) multi-channel flow model, and established an analysis method of "controlling factors → driving processes → modulating mechanisms." Our findings indicate that nutrient regime variations, including NO3- concentration, N:P ratio, and dissolved organic matter (DOM) accumulation, are controlling factors, whereas differences in kinetic processes, including uptake, assimilation, degeneration, excretion, and decomposition between diatoms and dinoflagellates, are driving processes. This study improves our understanding of how coastal phytoplankton composition responds to nutrient regimes associated with global climate change and their management.