Plant endemic species are the result of continuous evolution under the combined action of long-term climatic and geological conditions. There are 534 bamboo species in China, and 371 endemic species account for about 70% of all bamboo species. However, little is known about the differences in the rhizome evolution rate between endemic and non-endemic bamboos. Here, we collected morphological traits (height and leaf length) and environmental variables (including climate, space, and soil) of all 534 Chinese bamboo species to determine the relative contribution of environmental factors and traits of bamboo rhizome evolution with different endemism by structural equation modeling. We found that endemic bamboo had a higher speciation rate than non-endemic bamboo. The distribution centers of sympodial bamboos are mainly located in the mountain range of southwest China, while amphipod and monopodial bamboos are distributed with higher latitudes farther east in China. The height of non-endemic sympodial and monopodial bamboos was significantly higher than endemic sympodial and monopodial bamboos. The leaf length of non-endemic sympodial bamboos was significantly higher than endemic sympodial bamboo, while the leaf length of non-endemic amphipod bamboo was significantly lower than endemic amphipod bamboo. Environmental factors and traits explain 47% of the evolutionary variation of non-endemic bamboo species, while they explain 17% of that of endemic bamboo species. Longitude, latitude, and leaf length were the critical factors in the rhizome evolution of non-endemic bamboo, while longitude and height were the critical factors in the rhizome evolution of endemic bamboo. Our results imply that for higher species formation rates, endemic bamboo should be more concerned than non-endemic bamboo in the process of bamboo rhizome evolution. It will likely appear that new non-endemic bamboo species have a short leaf length in higher latitudes and farther east in China (the lower Yangtze plain), as well as new endemic bamboo species with a low height farther east in China (the Wuyi Mountains). Meanwhile, ancient non-endemic bamboo with a long leaf length in Yunnan Province and ancient endemic bamboo with a high height in the Hengduan Mountains may be more likely to become extinct. Our findings highlight the importance of understanding the difference in the rhizome evolution of endemic and non-endemic bamboos, which provides new insights into the conservation of Chinese bamboo biodiversity.