Background: Sapindus is an important biodiesel, biomedical, and multifunctional economic forest species in Asia, however its germplasms have been persistently damaged or lost. It is imperative to conserve the diversity of Sapindus. This study aimed to reveal the potential habitat distribution patterns of Sapindus mukorossi, Sapindus delavayi, and Sapindus rarak in response to current environment and future climate change, and identify hotspots of habitat degradation/expansion to facilitate climate change-adaptive biological conservation. Methods: Using current environmental data and future climate projections (2021–2100), we simulated the present and potential future habitats of Sapindus mukorossi, Sapindus delavayi, and Sapindus rarak in east and southeast Asia using a maximum entropy (MaxEnt) model that was developed based on 2041 occurrence records. Results: The model showed that precipitation may play an important role in framing the potential habitats of Sapindus; however, S. delavayi was more sensitive to minimum temperatures (-2 °C to 3 °C) and elevation (1200-2000 m), while S. rarak was more demanding in terms of solar radiation (annual mean Uvb of 4600 to 5000 J/m2/day). Under the current environment, S. mukorossi has the widest suitable habitat distribution (250.24 × 104 km2), followed by that of S. rarak (173.49 × 104 km2), and S. delavayi (78.85 × 104 km2). Under future climate change scenarios, the habitat distribution of S. mukorossi will expand and contract, that of S. delavayi exhibited significant expansion. In contrast, future S. rarak habitat distribution exhibited significant contraction. Conclusions: There were significantly distinct ecological adaptations among Sapindus mukorossi, Sapindus delavayi, and Sapindus rarak in east and southeast Asia. The contraction areas should be subject to germplasm collection and ex situ conservation preferentially. The modelled unchanged areas should be used for potential future Sapindus mukorossi, Sapindus delavayi, and Sapindus rarak conservation and utilization.