In order to identify and assess salt tolerance of japonica rice germplasm at seedling stage, salt stress treatment, by using Yoshida culture solution containing 125 mmol/L NaCl, was applied for analyzing 165 japonica rice germplasm accessions. Several parameters including salt tolerance score, leaf damage percentage, seedling height, root length, SPAD value, shoot fresh weight, root fresh weight, shoot dry weight and root dry weight as well as shoot water content were measured. The results revealed significant positive correlations between salt tolerance score and relative seedling height, relative SPAD value, relative shoot fresh weight, relative root fresh weight, relative shoot dry weight, relative root dry weight, relative plant dry weight and shoot water content. Meanwhile, salt tolerance score was found to be significantly negatively correlated with leaf damage percentage and relative root-shoot ratio. Principal component analysis (PCA) with 12 evaluation index suggested five major components, with a cumulative contribution rate of 86.473%. With membership functions and index weight method, a comprehensive evaluation value D for objectively assessing the salt tolerance of japonica rice germplasm resources at seedling stage was obtained. Subsequently, five rice germplasm (Bertone, Changbai 26, Yijing 12, Ningzi 629 and Xiaohubandao) showing the top five D value at the seedling stage were selected. Furthermore, cluster analysis assigned 165 japonica rice germplasm into four groups. For examples, salt-sensitive germplasm accessions were mainly found in group-I; the germplasm genotypes showing weak salt-tolerant were resided in group-II; the group-III contained only one salt sensitive cultivar (Suxuan 2); the group-IV was largely consisted of weak salt-tolerant and salt-tolerant germplasm genotypes. Taken together, five parameters including salt tolerance score, relative root length, relative shoot dry weight, relative root dry weight and shoot water content, were deployed as important indicators, in order to identify salt-tolerant japonica rice germplasm at seedling stage. The results gained from this study?provide a theoretical foundation for screening and identifying the salt-tolerant rice germplasm resources.