To understand the variation characteristics of fruit phenotype of jujube resources in Inner Mongolia, and reasonably select excellent resources, statistical analysis, variance analysis and correlation analysis were used to compare and analyze the 10 jujube natural populations in this study. And their kernel-using value was comprehensively evaluated by hierarchical grey relational method. The results showed: (1) The jujube resources were rich in genetic variation of fruit characters among and within populations. The average coefficient of 16 fruit traits was 17.96%, while kernel-related traits were particularly high abundance. (2) Correlation analysis showed that there were different degrees of correlation between the fruit、stone and kernel. Furthermore, fruit and kernel size have significant positive correlation with longitude and latitude, but significant negative correlation with altitude. The single kernel content rate was significant negative correlation with the mean annual temperature. The effective medicinal components of kernel had no significant correlation with latitude、altitude、longitude and average annual rainfall. (3) The comprehensive evaluation model of jujube kernel-using value was established by hierarchy-gray correlation method. The evaluation results showed that the comprehensive quality for kernel-using from 10 jujube natural populations was: P8＞P5＞P1＞P7＞P2＞P9＞P4＞P3＞P6＞P10. Among which, the population from Hangjinqi-Wujier of Erdos have obvious advantages compared with other populations. This study provides a scientific basis for the protection and utilization of jujube resources, and provides germplasm basis for the breeding of kernel varieties.