As a transcription repressor, the bmi1b gene plays an important role in maintaining the self-renewal and proliferation of many stem cells. This study identified single nucleotide polymorphisms of bmi1b and conducted an association analysis with bighead carp (Hypophthalmichthys nobilis). The bighead carp bmi1b gene has 5800 bp in length including nine exons and eight introns; therefore, its amino acid sequence is evolutionarily conserved. The hypothalamus exhibited the greatest spatial expression of bmi1b in the tissues of adult bighead carp. During the embryonic development and larval stages of bighead carp, this gene was highly expressed from the unfertilized egg to the blastocyst stage, whilst its expression was significantly lowered after the gastrula stage. Two single-nucleotide polymorphism (SNPs), g. 5224 T＞A and g.5550 C＞T, were obtained at the 3′ UTR of bighead carp bmi1b by direct sequencing of polymerase chain reaction (PCR)-amplified products. The results from genotyping these two SNP loci in 169 fish from a multi-family population of bighead carp and their correlation with growth and body type highlighted three key findings: (1) g. 5224 T＞A was significantly associated with body weight and head height (P＜0.05); (2) g. 5224 T＞A was significantly associated with body height and head length (P＜0.01); and (3) g.5550 C＞T had no significant association with body weight and body type traits. Allele combination analysis of the two SNPs showed that the diplotype D2 (AT CC) was the dominant genotype combination and its mean body weight and size traits were significantly higher than other diplotypes. These results provide a valuable reference for further research on the function of the bmi1b gene in fish. Additionally, the SNP markers of the bmi1b gene and their dominant genotype show good potential in molecular breeding studies of growth and body type traits in bighead carp.