The cold tolerance at the booting stage and main agronomic traits of 347 improved japonica rice varieties were evaluated under natural low temperature and cold water irrigation, which were from nine countries and eleven provinces of China, and the cluster analysis of the varieties was conducted. The result showed that main agronomic traits associated with cold tolerance and cold water response index (CRI) among the varieties had significant differences under natural low temperature and cold water irrigation. Under both conditions the cold tolerance at the booting stage (Seed setting rate) and CRI of the improved japonica rice varieties from Yunnan and Japan were higher than those of other countries or provinces. From the overall trend, the cold tolerance at booting stage of the varieties from relatively higher latitude of north provinces were stronger than those from relatively low latitude of southern provinces except few provinces under natural low temperature. However, under cold water irrigation, the relationship between the cold tolerance and origin of varieties was not close and did not show a regularity. In addition, the cluster results of the improved japonica rice varieties were connected to geographical location. Moreover, the results was connected more closely to origin of varieties under cold water irrigation than natural condition.