Climate change and human activities are expected to have a profound impact on the distribution of species, especially for narrow distributed species. Sinojackia is endemic distributed in eastern China, and all species are listed in Chinese protected wild species. Here, we reconstructed the phylogeny and estimated the divergence time of Sinojackia based on whole plastomes, conducted the niche evolution and predicted the potential habitat area of Sinojackia from LGM to future. Our results strongly supported the monophyly of Sinojackia based on the whole plastomes. This genus originated at middle Miocene and diversified since the late Miocene. Aridity index was a highest significant factor for their niche evolution, and the niche evolution rate increased slow since its divergence. Precipitation of warmest quarter was a main environmental variable affecting the distribution of Sinojackia in LGM, while human footprint is the main variable in near-current and 2081-2100. Compared to the current distribution of Sinojackia, the highly suitable distribution area contracted in LGM, but expand in the 2081-2100. This study provides potential areas for in situ conservation of Sinojackia.