The aim of this study was to establish an scientific evaluation system for fruit radish quality. 8 quality indicators were measured for 23 varieties, such as Meinong, Qiaotouqing and Chunbulao. The indicators included root weight, root shape index, water content, crispness, soluble solids, crude fiber, isothiocyanate and vitamin C. These data were analyzed by variation correlation analysis, principal component analysis and system cluster analysis. 23 varieties of fruit radish were analyzed by variation correlation; 8 indicators were compressed into 6 integrated variables using principal component analysis. Finally, the main evaluation indicators of fruit radish were determined by using cluster analysis and correlation analysis. The results indicated that the range of variation coefficient was from 1.64%—89.99%. Water content, crispness, soluble solids, crude fiber, isothiocyanate were important components of fruit radish quality, playing a major role in the quality. These 8 indicators were closely related and relatively independent. Water content was significantly and positively correlated with crispness; soluble solids and crude fiber were significantly and negatively related to vitamin C; crispness was significantly and positively correlated with crude fiber and vitamin C. Based on the above results, 4 representative indicators were used for evaluating fruit radish quality, that is water content, crispness, soluble solids, crude fiber, which could reflect the most information of fruit radish quality.