Abstract: To grope categorizing method in japonica rice, and calculate the genetic distance of quantitative characters, and study the relationship between genetic distance and heterosis. The key components analysis and cluster analysis were performed for 12 quantitative characters of 30 japonica rice germplasms. Study of the relationship between genetic distance and heterosis were carried out by the graphics. 12 quantitative characters of 30 japonica rice germplasms were concluded to 5 main factors. The contribution of the 5 main factors to total variation of population studied accounted for 86.84%. During evaluating the japonica rice germplasms , the total number of grain per panicle and the number of the filled grain per panicle should be selected firstly. Then the maximum tiller number of the population should be chosen, and finally the growth stage and the vegetative character and the plant type etc. be adjusted. 30 japonica rice germplasms were classified into 5 groups. There wasn’t definite relationship among the geographic distance and the pedigree and the genetic distance. The relationship between the genetic distance and the teterosis was complicated. The largest genetic distance didn’t mean the best heterosis. To evaluate japonica rice germplasms, geography origin and pedigree shouldn’t be only depended on. Selecting parents with medium genetic distance may probably gain stronger heterosis.