Through analyzing the phenotypic differences at agronomic traits under salt stress and control growth conditions, the rice cultivars showing salt-tolerant have been obtained valuable in breeding for new rice varieties adapting to the saline-alkali fields. In this study, we conducted a screening for salt-tolerant elite rice genotypes using 120 rice genotypes in China. This experiment was performed using hydroponic culture using five treatments (salt concentration: 0‰, 1.5‰, 3‰, 4.5‰ and 6‰) in the whole growth period. Dozens of phenotypic traits (Plant height, main stem thickness, root length, the length of top first leaf, the width of top first leaf, the length of top second leaf, the width of top second leaf, green leaf number, spike length of the main stem, stem dry weight, leaf dry weight, panicle dry weight, root dry weight, ground dry weight, root shoot ratio, spike number, spike grain number, thousands seeds weight, seed setting rate and theoretical yield of each rice variety) were quantified at the maturity stage. First, the optimal salt concentration was determined by the quartile difference method. Secondly, principal component analysis was carried out for each salt-tolerant coefficient under the optimal screening salt concentration. Based on the principal component analysis, membership function value and comprehensive evaluation value (D value) was obtained by using fuzzy function method. Stepwise regression analysis and correlation analysis were carried out with D value and salt-tolerant coefficient value of each variety. Finally, the D values of each rice variety were systematically analyzed by the Euclidean distance and Ward method. The results showed that 6‰ salt concentration was the best salt concentration for screening. The regression equation was obtained through principal component analysis, membership function analysis and stepwise regression analysis: D value = 0.152 + 0.004*LT1 + 0.005*GDW + 0.007*SL - 0.027*MST + 0.047*WT1.The results of systematic cluster analysis showed that 11 rice varieties with highly salt-tolerant, 19 salt-tolerant, 24 medium salt-tolerant, 45 salt-sensitive, and 21 highly salt-sensitive were classified (Euclidean distance 5).The optimal salt concentration was 6‰ during the whole growth period of hydroponics. The salt-tolerant of rice could be quickly identified by using the regression equation by measuring the length of top first leaf, the width of top first leaf, main stem spike length, ground dry weight and main stem thickness of rice at maturity. Collectively, this study identified highly salt-tolerant rice germplasm resource which laid a foundation for future exploring salt-tolerant genes and breeding for rice varieties.