Emmenopterys henryi is a Chinese endemic relict, autogenous, and endangered tree mono-species which is endemic to endangered China. To investigate the potentially geographical distribution pattens and its changes since the Last Glacial Maximum (LGM), it is essential to research the phylogeny of flora, changes of paleoecology and paleoclimate in subtropical China. We used the distribution data of Emmenopterys henryi and climatic variables to construct models of for potential geographical distribution in the LGM, Mid Holocene (MID), current (1960-1990), and future (2061-2080) of Emmenopterys henryi based on MaxEnt model and spatial analysis techniques of ArcGIS. The distribution of each climatic factor and the rule of changes of geographical distribution patterns were quantitatively investigated. The results showed that about 197.575×10⁴ km² area was suitable for Emmenopterys henryi to exist. It's mainly located in the mountainous region around Sichuan Basin, Wuling mountainous area and Wuyi mountainous area. The average temperature of dry season, rainfall of rainy season and rainfall of the coldest season are three most influential factors of determining distribution of Emmenopterys henryi. In LGM, Emmenopterys henryi were widely distributed in subtropical China, then the suitable area for them to exist was contracted landward. In MID, it continued to be contracted and move to high latitudes. Now, the area suitable for Emmenopterys henryi to exist was contracted and moved to high latitudes and the west area continuely in different emission circumstances. In conclusion, there is a trend of contracting and moving to high latitudes and the west area for the area suitable for Emmenopterys henryi to exist. It is recommended to carry out real-time monitoring, artificial breeding and ex situ preservation to preserve the existing Emmenopterys henryi.