Sapindus mukorossi Gaertn is a traditional and important virescencetree species in the south part of China with rich saponins in peel and rich oil in seed. This tree specie is one of the newly-developed woody oil species that were approved by the State Forestry Administration of China. The objectives of the present study were investigating phenotypic variation of 10 fruit and seed traits among 13 natural populations of S. mukorossi and disclosing the relationship between phenotypic variation and geographical factors. Variance analysis, multiple comparison, correlation analysis and principal component analysis were used to examine morphological diversity among and within populations based on data of 10 phenotypic traits. Results showed significant variation in fruit and seed traits within and among populations. The degree of variation in the 10 traits was significantly higher among populations than that within populations. The averaged coefficient of variation (CV) for the 10 traits was 7.34%. The mean phenotypic differentiation coefficient for the 10 traits was 62.21%, and the variation within populations (27.46%) was lower than that among populations (39.93%), indicating that variance among populations was the main source of the phenotypic variation in S. mukorossi. There were significant difference in most traits among populations, and most traits exhibited larger degree of differentiation in the marginal populations. Geographically continuous variation was not detected, and the differentiation of most traits were not consistent within the populations. Seed morphology was largely influenced by ecological factors of populations. The seed morphology in northwest area is near oval, whereas the seed morphology in eastern and southern area is near sphericity. Altitude and annual average temperature were significantly corelated with major traits of fruit and seed, idicating that altitude and annual average temperaturethe were the main genographical and ecological factors and they interactively contribute to variations of fruit and seed phenotypic traits among populations and within populations. The multiple variations among and within populations provided insights and guidelines for genetic conservation and utilization of S. mukorossi germplasm resources.