Growth is one of the most important traits of commercial fishes. Bighead carp are intensively cultured in China and some Asian countries; however, the genetic basis of growth is less understood. In this study, we calculated the heritability of growth-related traits in a mixed population of 840 bighead carp and estimated growth-related QTL in a family of bighead carp using bulked segregation analysis of resequencing data. High phenotypic (0.70–0.95) and genetic (0.77–0.97) correlations were found between all growth-related traits. Estimated heritability of 0.20 ± 0.11, 0.28 ± 0.14, 0.32 ± 0.16, 0.14 ± 0.11 and 0.12 ± 0.09 were obtained for body weight, body height, head length, total length, and body length in bighead carp with seven month old. In the BSA analysis for progeny with extreme segregated body weight of a single family, three regions located in LG01, LG11 and LG22, respectively with a total length of 17.84 Mb which were obtained according to correlation thresholds. Annotation of genes within this region yielded 120 and 61 nonsynonymous and code-shifting mutations, respectively, by comparing SNPs and InDel between the two growth difference groups. Finally, 14 candidate genes, including T-box transcription factor 3, transcription factor E2F2, paired box gene 9, and fibroblast growth factor 6b were identified. Association analysis and mRNA levels revealed that paired box gene 9 and fibroblast growth factor 6b were significantly associated with growth-related traits in extreme growth samples. These results provide insights into the genetic mechanisms underlying the regulation of growth and development in the bighead carp. •Calculated the heritability of growth traits in a mixed population of 840 bighead carp.•A region of 17.84 MB was located by BSA analysis between groups of weight extremes.•181 genes with genotypic differences were annotated and 14 candidate genes were identified.•Pax9 and lrp6 were significantly associated with growth by mRNA expression and SNP association analysis.