HD-Zip III transcription factors are known to play roles in regulating shoot apical meristem (SAM) and axillary meristem (AM) development, exerting direct effects on plant architecture and branching. However, the HD-Zip III (BjuHDZ) gene family has not been systematically characterized in Brassica juncea L. (B. juncea). Therefore, in this study, we performed a comprehensive bioinformatics analysis of the BjuHDZ gene family and identified a total of 20 members. These genes were randomly and unevenly distributed across the 16 chromosomes of B. juncea, and their encoded proteins exhibited divergent physicochemical properties. Through phylogenetic analysis, the 20 BjuHDZ proteins were divided into five subgroups (REV, HB8, HB9, HB14, and HB15). Conserved exon–intron organization and motif profiles were observed within each BjuHDZ gene subgroup. Furthermore, their promoter sequences harbored a wide array of cis-elements implicated in light responsiveness, hormonal regulation, stress tolerance, and growth/development. The qRT-PCR analysis showed that the expression levels of BjuHDZ7, BjuHDZ13, and BjuHDZ15 were significantly upregulated in the middle and upper axillary buds of two pairs of multi-branching (Bj02 and, Bj08) accessions. Meanwhile, BjuHDZ17 was highly expressed in the upper, middle, and lower axillary buds as well as in the SAM of both multi-branching materials. Taken together, these findings lay a foundation for further investigation into the biological functions of BjuHDZ genes in B. juncea.