The spatial distribution of soil phosphorus fractions (SPFs) in the Three Gorges Reservoir area (TGRA) is crucial for evaluating water quality and lake eutrophication in the lower reaches of the Yangtze River. Besides, it is also unclear whether climate change and rising elevation will alter the risk of phosphorus loss in this region. To address this knowledge gap, soil samples were extensively collected in Chongqing section of the TGRA and extracted SPFs using a rapid sequential extraction method. Results indicated that Ustifluvents, Haplustepts, and Kanhaplustults are suitable for cultivation but also prone to the risk of phosphorus leaching due to high labile phosphorus concentration. Increased temperature positively affected labile and medium-stable phosphorus, while increased precipitation accelerated phosphorus leaching. Solar radiation has significant effects on medium-stable and stable phosphorus. Additionally, multivariate and redundancy analysis showed that different SPFs were influenced by various environmental factors, but elevation is the predominant factor affecting most SPFs in the TGRA. Northeastern TGRA and areas with lower elevations on both sides of the Yangtze River were more susceptible to phosphorus leaching. This study is expected to provide decision-makers with references and help manage the regional environment in the context of climate change.