In order to study the genetic diversity and genetic structure changes of the selected population through complete diallel crossing in Sanjiang River system, six groups of hybrid Progenies (PearlRiver♀×Heilongjiang River♂(ZH), Heilongjiang River♀×Pearl River♂(HZ), Yangtze River♀×Pearl River♂(CZ),Yangtze River♀×Heilongjiang River♂(CH),Pearl River♀×Yangtze River♂(ZC),Heilongjiang River♀×Changjiang River♂(HC),Heilongjiang River♀×Heilongjiang River♂ (HH), Yangtze River♀×Yangtze River♂ (CC) and Pearl River♀×Pearl River♂ (ZZ)). The microsatellite sequence genetic variation of 9 grass carp populations was analyzed. The results showed that the average number of alleles N_a) was (5.75-12.33), the average number of effective alleles N_e) was (3.8077-6.3065), the average observed heterozygosity (H_o) was (0.7682-0.9036), the average expected heterozygosity (H_e) was (0.8385-0.6210), and the polymorphism information content (PIC) of 12 microsatellite loci in 9 populations of grass carp was high. They were 0.892, 0.823, 0.857, 0.894, 0.927, 0.859, 0.850, 0.859, 0.859, 0.907, 0.929, 0.879, 0.749 and 0.869 respectively, showing high polymorphism loci (PIC is from 0.749 to 0.929). UPGMA phylogenetic tree based on Nei's genetic similarity and genetic distance of different populations showed that among 9 populations, Heilongjiang River♀×Pearl River♂(HZ)and Yangtze River♀×Pearl River♂(CZ) clustered first, indicating that the genetic relationship between the two combinations was closer, and the genetic distance between Pearl River♀×Heilongjiang River♂(ZH)and Heilongjiang River♀×Changjiang River♂(HC) combinations was the farthest. The purpose of this study is to provide reference value for grass carp breeding in the future, lay a foundation for further species renewal and genetic improvement of grass carp, at the same time, provide a solution to the current degradation of grass carp germplasm, and provide a theoretical basis for the breeding of grass carp fine strains.