Idesia polycarpa is an important woody oil and biomass energy tree species in China, the development of germplasm resources and research of genetic variation on I. polycarpa are of great significance. The phenotypic traits were investigated and determined, and variation among and within populations were analyzed on nine natural groups in the distribution zone of I. polycarpa. The results indicated that there were significant differences in age, growth and yield traits of I. polycarpa from different population, especially in yield. There were rich variations in fifteen phenotypic traits including leaf length. These variation appeared among and within populations, and with similar contribution rate (31.99% and 30.82%). The variation of fruit traits were much more obvious in phenotypes, and the variation coefficients such as number of fruits per grain, which were closely related to yield, were up to 38%. The rich genetic variation of I. polycarpa provides many advantages for the development and utilization of germplasm resources, selecting and breeding.