Hainan Island in southern China is situated within the Indo-Burma biodiversity hotspot, and has attracted the attention of evolutionary biologists, geologists, and biogeographers. However, the palaeogeography of Hainan Island and its relationship with mainland China remains contested. In this paper, we report RAD-seq data for Engelhardia roxburghiana populations from Hainan Island and adjacent mainland areas to identify genetic diversity, structure, divergence time, and demographic dynamics over geologic time. Findings were assessed using climate model data to constrain suitable distribution areas. Results indicate that E. roxburghiana dispersed from the Chinese mainland to Hainan Island via a hypothetical land bridge during the late Eocene so that the drift of Hainan Island was impossible. We cast doubt on the hypothesis that Hainan Island was connected to Vietnam and Guangxi at this time. We emphasize that higher genetic diversity in the Yunnan-Guizhou Plateau and Chiang-nan regions is the result of mixed populations or the existence of refugia, and lower genetic diversity in the Indochina Peninsula is due to a historical bottleneck. From the late Eocene to Oligocene, the arid belt that dominated East Asia retreated, facilitating the expansion of E. roxburghiana from the Indochina Peninsula to southern China. The main diversification of E. roxburghiana occurred in the Miocene following the strengthening precipitation within the East Asian Summer Monsoon. Climatic oscillations during the Quaternary led to the contraction of E. roxburghiana in the Indochina Peninsula, with expansion after Last Glacial Period (LGP; 119 to 11.7 ka). Southern China has served as a refugium and continues to do so in the future. In summary, our study elucidates the evolutionary trajectory of E. roxburghiana through large-scale sampling, providing insights into the palaeogeography of Hainan Island and itsbiogeographic relationships with adjacent mainlands.