Drought is one of the major abiotic stress factors limiting rice production. Clarifying the identification methods for drought tolerance at the seedling stage and screening drought-tolerant rice varieties are of vital importance for promoting rice production. In this study, 16 conventional late japonica rice varieties from Zhejiang Province were selected and cultivated in artificial climate chambers. Subsequently, drought stress was imposed using a 25% PEG-6000 solution, and various indicators were measured in detail, including survival rate, seedling length, root dry biomass, shoot dry biomass, root-to-shoot ratio, root diameter, total root length, and root surface area. The results showed that under drought stress, the average values of survival rate, seedling length, root dry biomass, shoot dry biomass, root diameter, total root length, and root surface area decreased by 29.08%, 16.51%, 14.72%, 26.89%, 10.39%, 7.86%, and 26.84%, respectively, while the root-to-shoot ratio increased by an average of 15.29%. Based on the coefficient of variation of the relative values of these eight traits, it was concluded that survival rate, root dry weight, total root length, and root surface area could serve as key indicators for evaluating drought tolerance at the seedling stage in conventional late japonica rice varieties from Zhejiang Province. To further verify the reliability of these indicators, fuzzy membership function analysis and principal component analysis were employed to assess the drought resistance of the varieties. The results showed a 100% overlap between the two methods, confirming the feasibility of the selected evaluation indices. Additionally, cluster analysis classified the 16 rice varieties into four groups. Group I exhibited high drought tolerance, Group Ⅳ showed high sensitivity, while Groups Ⅱ and Ⅲ were characterized as moderately drought-tolerant and moderately sensitive, respectively. Based on the comprehensive evaluation, Zhekegeng 121 and Zegeng 136 were identified as highly drought-tolerant varieties, whereas Zegeng 99 and Zegeng 122 were classified as highly sensitive. This study not only provides a scientific and effective method for assessing drought tolerance in conventional late japonica rice varieties in Zhejiang Province, but also offers valuable parental resources for future breeding programs.