Insulin-like growth factor binding protein 3 (IGFBP3) is a most important gene regulating animal growth and metabolism. We isolated two IGFBP3 genes from Cyprinus carpio var.jian in this experiment. Eighteen SNPs loci were identified on IGFBP3a and IGFBP3b respectively. Eight SNPs were located at exons. PCR-RFLP was applied to detect genotypes of five SNPs (IGFBP3a intron 3_G-253T, IGFBP3b intron 2_G30T, IGFBP3b intron 3_A-341G, IGFBP3b exon 4_C54T, IGFBP3b exon 4_C72G) in 931 individuals (485♂,446♀). Correlation analysis between genotypes and weight gain showed that five SNPs were associated with female juvenile weight gain significantly (P<0.01 or P<0.05) and individuals with these five SNPs loci, TT, GG, AG, CC and CG genotype grew faster than other individuals. Only G30T was significantly related to male juvenile weight gain (P<0.05) and the GG individuals grew significantly faster than TT ones. C72G and A-341G were significantly pertinent to adult weight gain (P<0.01 or P<0.05). Individuals with CG at C72G were significantly larger than those with CC and GG types. The AG and GG type male adult weight gain of A-341G were significantly higher than AA type, while AG type grew the fastest in female adult fish. G30T was significantly associated with female adult weight gain. The GG and GT type fish weight gain were significantly (P<0.05) higher than TT type, and the GG male adult individuals also grew obviously faster than other types. The GT type male adult weight gain of G-253T was significantly higher than GG and TT type (P<0.01), while no similar situation was found in female adult individuals. To conclude, with the fastest weight gain, GG type of G30T, AG type of A-341G and CG type of C72G could be used as molecular markers in C. carpio var. jian breeding. In addition, weight gain increased with the enrichment of molecular SNPs markers, consistent with the characteristics of quantitative traits.