As an important mariculture species in China, the rapid development of breeding industry of Japanese flounder (), lead to the breeding of Japanese flounder facing more and more serious problems at present, such as growth rate depression, fertility declined, resistance recession etc. In order to keep Japanese flounder aquaculture developing healthy and sustainability, it is necessary to get fast-growing Japanese flounder by crossbreedingand selecting. In this paper, four base stocks of Japanese flounder (), including Resistance stock (RS), Korea stock (KS), Resistance Japanese stock (RJ), Japanese Resistance stock (JR), were used to crossbreed and establish Japanese flounder families. The total length and body weight of these families would be measured, when they were about 19 months old. The SPSS system was used to analysis the data, at first. And then, estimated breeding values (EBVs) and other genetic parameters of total length and body weight were estimated by DMU package, based on the method of REML (Restricted Maximum Likelihood) and BLUP (Best Linear Unbiased Prediction) procedure. Results showed that, the phenotypic value of crossbreeding combination, KS (♂) × RJ (♀), was best among all the combinations. The heritabilities of Japanese flounder’s total length and body weight were 0.301 and 0.295, respectively, both of which were medium heritability. The correlations coefficient of breeding value and phenotypic value of growth traits were 0.838 and 0.827; both phenotypes of total length and body weight were statistically highly significant (<0.01) correlated to their breeding values, respectively. That is to say, the prediction result of breeding value reasonable accuracy was perfect. Comparing the means of breeding value of all combinations, we selected KS as male and RJ as female to breeding new species, because the two has the best breeding value relative to sex. By this method, new Japanese flounder variety growing rapidly could be brood successfully.