In the Changjiang (Yangtze) Estuary and its adjacent waters, phytoplankton undergo a characteristic succession during spring blooms, with the bloom typically shifting from diatom dominance to dinoflagellate dominance. This transition plays a key role in regulating regional biogeochemical cycling and ecosystem structure. Existing numerical models for this region remain limited in representing this succession. Some represent all phytoplankton as a single state variable, whereas others resolve multiple functional groups only in zero-dimensional box models. Neither approach can mechanistically capture the three-dimensional spatiotemporal dynamics of phytoplankton succession. To address this limitation, we developed a diatom–dinoflagellate dual-group ecological module for the Regional Ocean Modeling System (ROMS). The module explicitly represents 15 state variables and incorporates group-specific physiological traits, including distinct optimal growth temperatures, nutrient half-saturation constants, and optimal light intensities. It is fully coupled online with the three-dimensional hydrodynamic model. This modeling framework enables investigation of how temperature, water-column stratification, and riverine nutrient transport jointly regulate phytoplankton succession during spring blooms in the Changjiang Estuary.