This study aimed to evaluate the effect of genetic variation on expression of the calcineurin B gene (FcCN-B) in a breeding population of Fenneropenaeus chinensis. Thirty-two full-sib families of the G13 generation were randomly selected in 2018, and one individual from each family was randomly selected and rehomed to new cages (each cage contained 32 shrimps). The amount of feed was limited, and real-time PCR was used to detect the expression of the FcCN-B gene in the ganglion tissue of each shrimp. The results showed that the expression of the FcCN-B gene at the individual level had a positive skew distribution. The higher value of the mean (8.25) compared to the median (6.95) indicates the presence of individuals with extremely high expression. The maximum expression of individuals was 44.48 times the minimum expression of individuals, and the range was 43.48. The variation coefficient of FcCN-B expression at the individual level was 66.55%, whereas it was relatively small (19.31%) at the family level. The maximum expression was only 2.20 times the minimum expression at the family level. One-way analysis of variance showed that there were significant differences in the expression level of the FcCN-B gene between families (P<0.05). Heritability for FcCN-B gene expression, estimated using the animal models and their pedigrees, was 0.60±0.13. This indicates that there was a high level of genetic variation in the nuclear breeding population, and great genetic gain may be obtained. The results provide reference data to investigate the molecular mechanism of the competitive behavior and improve competitive ability in F. chinensis.