The application of cytoplasmic male sterile (CMS) line can effectively improve hybrids quality. In this study, the LncRNAs related to cytoplasmic male sterility in broccoli were identified by Illumina sequencing, and their target genes and expression characteristics were also analyzed. Meanwhile, the expression patterns of 16 randomly selected LncRNAs were detected by qRTPCR technology, which could provide new insights for further clarifying the mechanism of occurrence of male sterility involved by LncRNAs in broccoli. The results show that: (1) 4 326 LncRNAs related to male sterility were identified in broccoli. Among them, 37 LncRNA were differentially expressed between male sterility line and its maintainer. (2) 370 cistarget genes of these differentially expressed LncRNA were predicted, many of these target genes were transcription factors and bioproteins related to CMS. (3) XLOC_006651, XLOC_016660, XLOC_003494 and XLOC_013121 were highly expressed in early development stage of bud in male sterile line and its maintainer line, and then decreased gradually with development of bud; XLOC_021769 and XLOC_038964 showed a fallingrising expression pattern. And their expression were higher in male sterile line than that in maintainer line at different development stages of bud. (4) All sixteen LncRNA could be detected in pedicel, calyx, petal, stamen and pistil. XLOC_038964, XLOC_011575, XLOC_013157, XLOC_039677, XLOC_037356, XLOC_034182 and XLOC_017574 showed similar expression patterns, with low expression in stamen and pedicel, higher expression in calyx and petal, and the highest expression in pistil.