Aldolase is a glycolytic enzyme, which plays a key and pivotal role in glycolysis and glucose metabolism. And compared to aldolase A and aldolase C, aldolase B is involved in both glycolysis and gluconeogenesis. In this research, the two genomic sequence fragments are amplified according to two contigs cDNA fragments of ALDOB gene from EST database of grass carp(Ctenopharyngodon idellus). Then three nucleotides mutations were identified by using directly sequencing and blasting. The polymorphisms are C+687G, A117C and C+1042A, which are in exon 6, intron 7 and exon 8 respectively. C+687G is synonymous mutation and -A63C is non-synonymous mutation. 296 grass carps were used to genotype polymorphisms and then calculate the genotype and gene frequency by SnaPshot method. Frequencies of the AA genotype were 42.9%, 32.8% and 32.8% respectively, the AB genotype were 42.9%, 45.9% and 45.6% respectively, the BB genotype were 14.2%, 21.3% and 21.6% respectively. A general linear model was used to statistically analyze the relationship between ALDOB gene polymorphisms and major growth traits. The result indicated that the three different genotypes of C+687G site only showed significant association at body length/caudal peduncle ratio (P<0.05), while they showed no significant association at body weight. The three different genotypes of A117C andC+1042A sites showed significant association at body weight and so on (P<0.05). Three combinations of seven, three and seven diplotypes, with the minor allelic frequencies of above 3%, were constructed based on three SNPs in the experiment population. Association analysis indicated that three combinations of diplotypes were all significant association between diplotypes and body weight (P<0.05): the seven diplotypes of C+687G, A117C and C+687G, C+1042A showed significant association at body weight, body width and so on (P<0.05). And the three diplotypes of A117C and -43C, C+1042A showed significant association at body weight and space. Not only different genotypes of three SNPs sites, but also diplotypes showed significant association in major growth traits in grass carp. And the homozygous genotypes were higher than heterozygote genotypes in the main growth traits. As a result, ALDO B gene could be a candidate modifier gene for grass carp growth traits which could be useful for grass carp molecular breeding.