Growth traits are important economic traits in genetic breeding of aquaculture species. The combination of trait-related molecular markers and breeding can greatly accelerate the breeding process. In our previous research on the growth traits of Ctenopharyngodon idella, using the method of QTL mapping, we found two growth-related QTLs in the linkage group 1. Based on this, two pairs of the two QTL flanking markers (CID391_2, CID1512, CID973_1, and CID254_1) were used to analyze the 480 individuals of C. idella in the Yangtze River system in order to verify these microsatellite markers associated with growth traits in selected populations of grass carp. The results showed that:① the four microsatellite markers were highly polymorphic in this population (PIC> 0.50), among which the number of observed alleles (N_a) at each locus was 12 to 23, and the number of effective alleles (N_e) was 4 to 12, the observed heterozygosity (H_o) was 0.607-0.904, and the expected heterozygosity (H_e) was 0.751-0.902; ② by means of One-Way Analysis and multiple comparisons of the genotypes and the growth traits (body weight and body length) in the selected populations of C. idella, CID391_2 showed no significant difference between genotypes and the two growth traits in female individuals, while there was significant difference between genotypes and the two growth traits in male individuals; CID1512, CID973_1 and CID254_1 showed significant differences between each genotype and the two growth traits in female or male individuals. This study has verified microsatellite markers associated with growth traits in selected populations of C. idella. It will provide a basis for further research on QTL mapping in C. idella and the practice of molecular marker assisted selection (MAS) based on QTL mapping.