By establishing a distribution and environmental factor database of 21 typical harmful dinoflagellates in global waters, the MaxEnt model was used to predict shifts in the habitat of harmful dinoflagellates in Chinese waters under global climate change. The results revealed that offshore distance was the most important predictive factor and that surface seawater temperature (SST), primary productivity, and nitrate concentration were the key ecological factors influencing the distribution of harmful dinoflagellates. Under the low greenhouse gas emission scenario defined by the Intergovernmental Panel on Climate Change (IPCC), by approximately 2050, 17 of the 21 harmful dinoflagellate species in high-suitability areas (HSA) will migrate northward, six species will migrate eastward, and six species will expand their HSA. By 2100, approximately 18 of the 21 harmful dinoflagellate species in HSA will have migrated northward, seven species will have migrated eastward, and four species will have expanded their HSA. Notably, the HSA content of highly toxic Alexandrium minutum is expected to increase by 13.4% and 9.4% by 2050 and 2100, respectively. Under the high greenhouse gas emissions, there will be 17 species migrating northward, 6 species migrating eastward, and 4 species increasing in their size in HSA by 2050; moreover, there will be 16 species migrating northward, 2 migrating eastward, and 4 species according to their size of HSA by 2100. Specifically, the HSA of A. minutum is predicted to increase by 7.0% and 25.9% by 2050 and 2100, respectively. Notably, A. ostenfeldii, which is currently seldom present in the China seas, is predicted to exhibit an HSA in most coastal areas of the Yellow Sea, the Bohai Sea, the Hangzhou Bay, the Zhejiang Coast, and the Beibu Gulf of the South China Sea. Conversely, the HSA of Noctiluca scintillans, a typical red-tide species, will be reduced by 7%-90%. The northward migration of Karenia mikimotoi exceeded 100 km and 300 km under low and high greenhouse gas emission scenarios, respectively. These changes underscore the significant impact of climate change on the distribution and habitat suitability of harmful dinoflagellates, thus indicating a potential shift in their ecological dynamics and consequent effects on marine ecosystems.