The paralytic shellfish poison toxin (PST)-producing dinoflagellate, Gymnodinium catenatum, frequently blooms in China, posing a threat to food safety and human health. To understand the drivers of G. catenatum blooms and predict potential habitats for G. catenatum under climate change, samples from occurrence localities and environmental datasets from multiple agencies were aggregated and used to model the habitat suitability of G. catenatum in the China Sea using a maximum entropy model (Maxent). The accumulated variable contributions for the Maxent model were defined to measure the importance of key predictors in the model. The most important environmental variables were distance to the coastline, depth of seawater, and long-term average of the minimum annual temperature. This highlights the main reasons why G. catenatum blooms always occur in coastal waters. Occurrence probabilities higher than 0.66 were defined as habitats with high suitability for shellfish management and aquaculture. Projected habitats with high suitability in Haizhou Bay, coastal waters along the western Taiwan Strait, and Bohai Bay remained stable with increasing temperature by 2100, regardless of the IPCC Representative Concentration Pathways (RCPs). However, those in the China Sea would be reduced overall, leading to a northward movement of the center of integrated habitats. Habitats with a spatial area of >6000 km2 in the Bohai Sea, Yellow Sea, and South China Sea and >23,000 km2 in the East China Sea would be exposed to high risk under low greenhouse gas emission scenarios (RCP2.6).