Anthropogenic nutrient enrichment and accompanying stoichiometric imbalances have severely degraded coastal marine ecosystems globally, yet the long-term, non-linear responses of harmful algal blooms (HABs) to these shifts remain poorly constrained. Utilizing a coupled land-ocean modeling framework, we resolved the spatio-temporal dynamics of HABs in the Bohai Sea, revealing a structural shift in bloom patterns driven by escalating dissolved inorganic nitrogen (DIN) loads and persistent nitrogen-to-phosphorus disproportionality. Our simulations indicate that during 1980–2010, HAB coverage frequently exceeded 20% of the total Bohai Sea area, peaking at 28% in the 1990s, with Laizhou Bay emerging as the primary hotspot (71% affected area). Notably, we identified a multi-year ecological lag between initial nutrient loading and maximum HAB manifestation. Scenario analyses indicate that while dissolved inorganic phosphorus (DIP) reductions selectively suppress diatom blooms, mitigating dinoflagellate proliferation and systemic HAB risks requires a coordinated co-reduction of land-based DIN and DIP (by 70% and 50%, respectively). Furthermore, projection scenarios reveal that high nutrient stoichiometric ratios will persist despite aggressive loading reductions, a phenomenon we attribute to the legacy effect of benthic sediment recycling. These findings suggest that achieving long-term ecological recovery and effective HAB mitigation in semi-enclosed seas hinges upon a stoichiometrically balanced, multi-decadal management strategy for nitrogen and phosphorus.