Zinc finger, BED-type containing 6 (ZBED6) is a novel transcription factor that was identified and shown to act as a repressor of IGF2 transcription in skeletal muscle myogenesis and development. The aims of this study were to determine ZBED6 expression level and examine the association of the ZBED6 polymorphism with growth traits in Qinchuan beef cattle. The bovine ZBED6 mRNA was detected in eight tissues by quantitative real-time PCR (qPCR), being highly expressed in skeletal muscle. Three single nucleotide polymorphisms (SNPs) were identified the bovine ZBED6 by sequencing pooled DNA samples (Pool-Seq) and forced polymerase chain reaction-restriction fragment length polymorphism (forced PCR-RFLP) methods. In this study, we reported one mutation in the promoter and two missense mutations in the coding regions within the bovine ZBED6 gene, and the haplotype variability and extent of linkage disequilibrium (LD) in 817 individuals from the Qinchuan (QC) and Chinese Holstein (CH). We also investigated haplotype structure and linkage disequilibrium coefficients for three SNPs of ZBED6 in the study populations. The result of haplotype analysis of three SNPs showed that eight different haplotypes were identified in two breeds. The wild-type haplotype (Hap 1: GCA) and mutant-type haplotype (Hap 8: AGG) shared by two populations accounted for 29.8%, 57.5%, and 8.6%, 0% of all haplotypes observed in QC and CH, respectively. The statistical analyses indicated that three SNPs, 23 combined genotypes, and 8 haplotypes were significantly associated with different growth traits in the QC cattle population (P < 0.05 or P < 0.01). The mutant-type variants and mutant haplotype were superior for growth traits; the heterozygote diplotype was associated with higher growth traits compared to the wild-type homozygote. The results of this study suggest that the ZBED6 gene possibly is a strong candidate gene that affects growth traits in QC beef cattle breeding program.