Soil salinization serves as one of the important abiotic stresses, which might result in reduction of rice production. Breeding for salinity tolerance of rice is an effective way to prevent yield loss, and a comprehensive and precise evaluation of salt-toleranceduring the whole growth stage therefore becomes of interest. In this study, 19 rice varieties with levels of saline tolerance were tested under different salt concentration conditions, and 11 agronomic-related traits were investigated. Furthermore, the optimum concentration of salt tolerance was determined by using interquartile range method between varieties. The saline with maximum showed that the salt tolerance coefficient of 11 agronomic traits can be reduced to 3 principal components. By using the principal interquartile range between varieties was supposed to be the optimum stress environment. Because under this saline, the rice varieties shown the maximum genetic variation which measure by interquartile range between varieties. A series of comprehensive multivariate statistical analysis method, included principal component analysis, membership function analysis, stepwise regression analysis and cluster analysis, was used to explore the rational evaluation method of salt tolerance of rice during the whole growth stage. The results showed that under 0.3% salinity, between varieties，the salt tolerance coefficient of most traits shown the highest interquartile range. The0.3% salinity was the optimum concentration for identification saline tolerance in rice. The results of principal component analysis component contribution rate and membership function analysis, the three principal component values can be further simplified into the comprehensive evaluation index of rice saline tolerance: D value. D value can be used to evaluate the salt tolerance of rice germplasm simply and accurately. It can realize the comprehensive evaluation of salt tolerance of rice germplasm. In this study, we also used stepwise regression analysis to establish the optimal linear regression equation for the salt tolerance coefficient of 11 agronomic traits and D value: D=-0.365+0.647PL+0.152PN+0.274TW. Through stepwise regression analysis, the saline tolerance coefficient of spike length, spike grain number and total weight was the key indicator of D value. The saline tolerance of 19 rice germplasm can be divided into 5 grades by cluster analysis, corresponding to 5 salt tolerance grades of rice. It can be regarded as an important reference for salt tolerance evaluation of other rice germplasm. This study provides a comprehensive, objective and accurate method for the identification and evaluation of saline tolerance in rice during the whole growth stage, which can be used as an important basis for the identification and evaluation of saline tolerance in rice during the whole growth stage.