To understand the variation characteristics of fruit phenotypic traits of jujube resources in Inner Mongolia， China， and identify elite germplasm resources， this study deployed statistical analysis， variance analysis and correlation analysis to analyze the 10 jujube natural populations. The kernel value was comprehensively evaluated by hierarchical grey relational method. The results showed： （1） The average coefficient of 16 fruit traits was 17.96%， and muti-kernel content rate in stone has highest variation coefficient. The average range of fruit phenotypic traits variation among populations ranged from 10.69% to 31.01%， and the highest variation coefficient from Alxa Zuoqi-Tengger Eris population. （2） Correlation analysis showed that there were different degrees of correlation among the traits of the fruit， stone and kernel. Fruit transverse diameter and stone longitudinal diameter were positively correlated with longitude， fruit transverse diameter and stone longitudinal diameter were positively correlated with latitude， indicators mentioned above were negatively correlated with altitude. Single kernel content rate in stone was negatively correlated with the mean annual temperature. Kernel jujuboside A content and spinosin content have no significant correlation between latitude， longitude， average annual rainfall， and altitude. （3） The comprehensive evaluation model 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-Balagong have obvious advantages compared with other populations. This study provided a scientific basis for the protection and utilization of jujube resources and breeding of kernel varieties.