The shift of diatom dominance to combination of diatom and dinoflagellate dominance in the Bohai Sea (BS), China might be associated with the change of dissolved nitrogen (DN). This study combines field investigation, ship‐based microcosm experiments, a nitrogen biogeochemical model, and statistical analysis to reveal the impact of DN loading on the dominance of diatoms and dinoflagellates in the BS, considering the quantitative relationship between the algal growth/death and nitrogen migration/transformation processes. The diatom to diatom‐dinoflagellate shift was significantly associated with the DN regime shift of oxidized nitrogen (NO3‐N) to reduced nitrogen (NH4‐N and dissolved organic nitrogen [DON]) since the mid‐1990s. This phenomenon was supported by microcosm and numerical experiments: (a) Gonyaulax verior as a dominant dinoflagellate in the BS efficiently absorbed/assimilated NH4‐N, and it can also utilize DON derived from centric diatoms; Chaetoceros densus as dominant centric diatoms in the BS was able to absorb/assimilate NO3‐N, and it can also utilize DON derived from the Xiaoqing River; (b) The change in dinoflagellates/diatoms ratios was reproduced with the change in DN regime from the 1980s to the 2010s by the proposed nitrogen biogeochemical model based on localized parameters in the BS. Moreover, mixotrophism and stronger survival stability, associated with the faster NH4‐N and DONalgal uptake and slower decomposition of G. verior, also supported the shift from diatoms to diatoms–dinoflagellates during high variations in nutrient supply. This study infers the phytoplankton regime shift mechanism associated with the DN structure in coastal waters, providing a credible scientific basis for the shift from water quality‐based to ecosystem‐based environmental management.