Understanding the effect of climate changes on potential distribution of rare and/or endangered species is a primer of biology conservation. Phoebe bournei (Hesml.) Yang, a dominant tree in subtropical forest in eastern China, is one of the main sources for the "Golden-thread wood". P. bournei incorporates the value of the economy, landscape, and ecology. Now, it has been listed as Category II protected plants in the Chinese List of Wild Plants and as vulnerable according to the IUCN Red List of Threatened Species. A prediction of the impact of climate changes on the distribution of P. bournei will facilitate the utilization of germplasm resources as well as its evolutionary history. The 123 occurrences data covering the whole distribution range of P. bournei in China were obtained and the eight main bioclimatic variables were selected in this study. We used the maximum-entropy (Maxent) model for predicting potentially suitable habitat for P. bournei under paleoclimate, current and future climate background. The maxent model was highly accurate with a statistically significant AUC of 0.8. The results showed that the suitable region for P. bournei was Zhejiang, Fujian, Jiangxi, Guangdong, Guangxi, Hunan, Hubei, and Chongqing. From the area of current distribution, with a total area of 1047314 km², 233142 km² (22.26%), 360626 km² (34.43%), and 453545 km² (43.31%) were highly suitable area, moderately suitable habitat area, and poorly suitable habitat area for P. bournei in China, respectively. The variation coefficient of temperature (Bio4), the warmest month of temperature (Bio5) and precipitation of the driest quarter (Bio17) were the major climatic factors determining its suitable region. In addition, P. bournei retreated to many mountains in eastern China, such as Wuyi Mountain, Zhejiang-Fujian hills, Wuling Mountain, Xuefeng Mountain, and the mountains near Hunan-Guizhou-Guangxi borders during the Last Glacial Maximum (LGM) period. Under global warming, the suitable habitat for P. bournei will be at risk of fragmentation or even loss by 2050 and 2070. The predicted suitable areas of P. bournei located in Jiangxi and Fujian will be more seriously fragmented, and ones located in the Hunan-Guizhou border might be disappeared. To protect this valuable timber tree, we suggested should use in-situ and ex-situ conservation strategies. Especially, the wild populations should be taken in-situ conservation strategies, such as Guanshan population located in Jiangxi, Shaxian population located in Fujian and Chebaling population located in Guangdong province. This study would provide theoretical suggestions for the protection, cultivation management, and sustainable utilization of P. bournei resources to face the challenge of global climate changes.