Abstract: In order to study the diversity, variation and differentiation of fruit phenotypic traits in natural populations of Idesia polycarpa, and to explore the comprehensive evaluation methods, the Shannon-weaver diversity index analysis, nested variance analysis, multiple comparison, principal component analysis and cluster analysis were performed on 15 fruit phenotypic traits of 32 individual plants from 3 natural populations of I. polycarpa in Guizhou for providing scientific basis for conservation, utilization, selection and breeding of natural populations of I. polycarpa. The results showed that the Shannon-Weaver diversity index of 15 fruit phenotypic traits in I. polycarpa ranged from 1.944 to 2.090, with an average of 2.019, indicating that the fruit traits in I. polycarpa had rich diversity. The variation coefficients of the 15 traits ranged from 5.67% to 38.57%, and the number of full seeds per fruit（38.57%）, grain weight per ear（28.72%）, grain weight per ear（26.63%） and grain number per ear（26.29%）had the greatest variation.The variation of fruit shape index（5.67%）and fruit oil content（7.88%）was small.There were significant or extremely significant differences among and within populations among the 15 traits,indicating that there were abundant variations among and within populations of these traits.Intra-population variation（38.24%）was higher than inter-population variation（17.76%）,and the average phenotypic differentiation coefficient between populations was31.79%.And,intra-population variation was the main source of phenotypic variation of fruit traits in I.polycarpa.Additionally,the results of principal component analysis showed that the cumulative contribution rate of the first six principal components reached 85.38%,representing most of the phenotypic traits of paulownia fruit.Fruit size index,fruit weight,fruit peel weight,fruit longitudinal diameter,fruit cross diameter,fruit number per ear,fruit weight per ear and fruit weight per ear were the main factors that caused the fruit phenotypic differences of I.polycarpa.Comprehensive evaluation results showed that single plant No.13 from P2 population had the highest comprehensive score,followed by single plant No.14 from the same population.Meanwhile,the single plant No.27 from population P3 had the lowest comprehensive score per plant,which were valuable materials for building germplasm resources with rich genetic diversity.According to the cluster analysis,32 individual plants could be divided into 4 groups when the Euclidian distance was 12,which had no close connection with geographical origin.