Abstract: 【Objective】 In this study, the main fruit characters of 52 pepper germplasm resources were investigated, and the genetic diversity and cluster analysis were carried out, in order to explore the germplasm resources that can be applied to genetic improvement, and lay the foundation for the innovation and sustainable development of pepper industry in Xinjiang. 【Method】 In this study, conventional detection methods and high performance liquid chromatography（HPLC） were used to investigate the main fruit phenotypic and quality traits of pepper. The genetic diversity, correlation, principal component and cluster analysis of all fruit traits of pepper were carried out by SPSS 25.0, R and origin 2018 software. Finally, the genetic cluster analysis of 52 pepper germplasm resources was completed. 【Result】 The results showed that in terms of genetic diversity, 13 main fruit characters in 52 pepper germplasm resources had different degrees of variation, among which the coefficient of variation of ventricular number was the lowest, 13.15%, the highest coefficient of variation of capsaicin content was 143.15%, the mean coefficient of variation was 58.19%, and the genetic difference of fruit quality traits was large; in correlation analysis, There was a significant positive correlation between fruit diameter, placenta size, pulp thickness, number of ventricles and single fruit weight. The color price was significant negatively correlated with capsaicin, Dihydrocapsaicin, total capsaicin and spicy degree. In the aspect of principal component analysis, the four main components were related to fruit weight, spicy degree, length and capsicum content respectively, with a contribution rate of 81.54%; in cluster analysis, the European distance was 7.5, The results showed that C.chinense, C.frutescens L and C.frutescens L could be separated from annual chilli. When the European distance was 2.1, 52 pepper germplasm could be divided into four categories. 【Conclusion】 Among the 52 pepper germplasm resources, there is relatively rich genetic diversity in fruit phenotype and quality traits, and there are some special germplasm materials that need to be excavated, which has important reference significance for the utilization and innovation of pepper germplasm resources in the later stage.