The Hemibarbus guttatus, a limited and vulnerable protected species in China, is currently facing significant challenges. The effects of climate change on the habitat of Hemibarbus guttatus remain insufficiently explored, especially with changing precipitation and temperature patterns potentially altering its potential habitable areas in southern river basins. This poses urgent concerns for its conservation and management. This study systematically compiles the distribution information of Hemibarbus guttatus, using WorldClim climate data (MIROC6 and MRI-ESM2-0 climate models along with SSP1-2.6 and SSP5-8.5 Shared Socioeconomic Pathways scenarios) and the Maximum Entropy Model (MaxEnt) to predict its potential habitable areas for the current period, the 2030s (2021–2040), and 2070s (2061–2080). Results indicate that the current habitable areas for Hemibarbus guttatus are mainly concentrated in Guangdong Province and Guangxi Zhuang Autonomous Region in Southern China, with temperature being the most significant environmental factor affecting its distribution. Under the energy-driven development scenario (SSP5-8.5), there is a notable expansion of potential habitable areas, with risks of invading coastal areas in Fujian and Zhejiang provinces. Research on the habitable areas of Hemibarbus guttatus and environmental variables affecting its distribution is of practical significance for its conservation zoning, management, and potential invasion prevention. It also provides a reference for other freshwater fish species in Southern China in response to climate change.