In this paper, We choosed 402 japonica varieties from 30 countries as experimental material, analyzed the Phenotypic differences and clustering features of the main Agronomic traits of Japonica varieties under natural condition and salt stress 。The Result Indicates that there were significant differences in the main agronomic traits of japonica varieties from different countries under salt stress ，including significant delay of the heading days, shorter culms length and panicle length, less number of effective heads and grains per head ，reduction of setting rate and dry-weight of seed 。 18 japonica varieties show a strong resistance to salt stress. By analyzation the main Agronomic traits and clustering，We found that salt tolerance and clustering result of japonica varieties have a certain correlation with geographic location, latitude and climate conditions in different countries .