Abstract: 36 special rice germplasm resources used as experimental materials, the effects of salt stress on the seedling biomass and root morphological parameters of different special rice varieties were analysed using the indoor hydroponic method. The results showed that 11 determination indexes were simplified into three major components, with a cumulative contribution rate of 71.43%, using principal component analysis（PCA）. With membership functions and index weight method, the three principal component values were further reduced to a comprehensive evaluation D value, for assessing the salt tolerance of different special rice germplasm resources at seedling stage. Four rice germplasms（Shandao, Y-9（Huangbai）, Zhebai and Heibaonuo） were selected. According to the D value, cluster analysis assigned 36 rice germplasm resources into five groups. The group-Ⅰ contained only one high salt-tolerant genotype（Shandao）; High salt-sensitive germplasm accessions were mainly found in the group-Ⅱ; The germplasm accessions showing salt-sensitive were resided in the group-Ⅲ; The group-Ⅳ was largely consisted of weak salt-tolerant germplasm; The germplasm genotypes with salt-tolerant were mainly clustered in group-Ⅴ. Combined with stepwise regression analysis, the optimal regression equation of 11 measurement indicators and D-value of was obtained: D=0.088+0.169×X_RS+0.144×G_RS+0.117×X_RR+0.048×G_RR-0.192×D_RA. In conclusion, relative shoot fresh weight, relative shoot dry weight, relative root fresh weight, relative root dry weight and relative average root diameter were deployed as important indicators to identify salt-tolerant special rice germplasm resources at seedling stage. The selected germplasm resources of special rice with strong salt tolerance at seedling stage were Shandao, Y-9（Huangbai）, Zhebai and Heibaonuo.