In this study, phenotypic characters, oil content and fatty acid composition in fruits of Sapindus spp. from sixty plus trees of thirteen provinces in China and Vietnam were screened and evaluated by the method of soxhlet extraction and gas hromatography. And on this basis, principal component analysis and correlation analysis on the above characters were carried out to analyse the variation of each characters, quantitatively evaluate the compound economic valuable characters and analyze the correlation between fatty acid variation and phenotypic variation. The results showed that: 1) a wide phenotype variation among sixty plus trees was presented. The variable coefficients of 100-fruit coat weight 100-seed kernel weight, seed kernel content, fruit lateral diameter and linolenic acid content were 33%, 32%, 29%, 29% and 33%, respectively, while oleic acid showed medium stability (4%); 2) Measuring the key economic characters with more variation by weight assignment method of principal component analysis, 7 repeated selection trees came from Guizhou, Guangxi, Guangdong, Hubei provinces were 42.86% and 41.86% higher in 100-fruit coat weight and 100-seed kernel weight compared with the average level of plus trees, thus the gain of economic traits of plus trees increased obviously. 3) The correlation analysis results showed that the unsaturated fatty acid had extremely significant negative correlation with kernel content and 100-seed kernel weight, while oleic acid had weak correlation with fruit characters. C20:1 had more correlation with fruit characters. The research provides important support to Sapindus spp. breeding process, and lays the foundation for bioenergy and saponin comprehensive exploitation and utilization.