Reduced available water resources have become the main limiting factor for the production of leafy vegetable, such as pakchoi, which can be effectively addressed by growing water-efficient varieties. Therefore, it is particularly important for evaluation and verification of drought tolerant varieties. In this study, 50 different varieties of pakchoi were detected for their morphological and physiological indicators under both normal-irrigated and water-deficiency environments. Based on systematic analysis of these evaluation indicators using different evaluation methods, the significant indicators were identified and the prediction model was established followed by validation of different drought tolerant of pakchoi varieties. The results showed that considerable differences were observed in all the indicators detected under conditions of water deprivation compared with normal irrigation. Frequency distribution revealed that the indictors sensitivity with significant changes to water-deficient conditions was ordered as follows: aboveground fresh and dry weight, followed by belowground fresh and dry weight, root volume, root length, root activity, and soluble sugar. Correlation analysis showed that each indicator was significantly or extremely significantly associated with other indices, indicating that there is a certain degree of association between the indices. Principal component analysis (PCA) turned 16 indicators into four independent components, with a cumulative contribution ratio of 80.147%. According to the results of drought tolerance comprehensive evaluation value (D-value) analysis and cluster analysis, 50 varieties were ranked in relation to drought tolerance and classified into five categories, among them Jinhui, Qingguan, Dongyue, Xiazhijiao, and Hanszifei, which were classified as highly drought-tolerant cultivars. Moreover, the stepwise regression model was established and demonstrated that soluble sugar, average root diameter, belowground fresh weight, root volume, and leaf number were selected as key indicators which can be used for screening and identifying drought-pakchoi varieties. Furthermore, the tolerance capacity of pakchoi varieties was further validated using one representative variety selected from five groups and treated with water-deficit stress. It was demonstrated that the established model was verified consistent with drought tolerance of pakchoi varieties, and tolerance capacity was closely related to increasing epidermal stomatal density, maintaining high photosynthesis, and increasing antioxidant enzyme activity to reduce damage (ROS). The results proposed the key drought tolerance indicators and evaluation methods, which provide the basis for the screening of leaf-vegetable varieties with different drought-tolerances, as well the identified varieties could be used for effective water-saving production.