The invasion and spread of alien aquatic organisms pose an increasing threat to ecosystem stability with the excerbated climate change. However, existing studies often paid little attention to the compound ecological risks of multi-species invasions driven by the combined effects of climate factors, topography, water quality, vegetation, and other environmental variables under future climate scenarios. To address the knowledge gap, this study focuses on Pomacea canaliculata and Eichhornia crassipes, utilizing the MaxEnt model and ArcGIS tools to analyze the dominant environmental factors influencing their invasion and spread in the middle and lower reaches of the Yangtze River, China. Additionally, this research predicts their potential suitable habitat distributions under current and future climate scenarios (SSP245 and SSP585) and compares their spatiotemporal response characteristics. The results show that the MaxEnt model performed with high accuracy for E. crassipes (AUC = 0.952) and good accuracy for P. canaliculata (AUC = 0.880). The habitat selection of E. crassipes is primarily influenced by isothermality, elevation, and temperature seasonality, while P. canaliculata is significantly affected by slope, elevation, and the mean temperature of the warmest season. In terms of current habitat distribution, P. canaliculata occupies a larger range than E. crassipes, with P. canaliculata exhibiting a widespread distribution mainly concentrated in the Hanjiang Plain and the Jiangsu-Anhui coastal plains, whereas E. crassipes follows a belt-like distribution pattern, primarily concentrated in Poyang Lake and the Yangtze River Delta. From 2021 to 2100, the suitable habitat of P. canaliculata is projected to expand under both SSP245 and SSP585 scenarios, with a more extensive and rapid expansion under the high-emission scenario (SSP585), where moderate-to-low suitability areas exhibit a pattern of sharp increases and decreases. In contrast, the suitable habitat of E. crassipes follows a trend of initial expansion followed by contraction under both climate scenarios.