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Background  The Polima ( pol ) system of cytoplasmic male sterility (CMS) and its fertility restoration gene  Rfp  have been used in hybrid breeding in  Brassica napus , which has greatly improved the yield of rapeseed. However, the mechanism of the male sterility transition in  pol  CMS remains to be determined.    Results  To investigate the transcriptome during the male sterility transition in  pol  CMS, a near-isogenic line (NIL) of  pol  CMS was constructed. The phenotypic features and sterility stage were confirmed by anatomical analysis. Subsequently, we compared the genomic expression profiles of fertile and sterile young flower buds by RNA-Seq. A total of 105,481,136 sequences were successfully obtained. These reads were assembled into 112,770 unigenes, which composed the transcriptome of the bud. Among these unigenes, 72,408 (64.21%) were annotated using public protein databases and classified into functional clusters. In addition, we investigated the changes in expression of the fertile and sterile buds; the RNA-seq data showed 1,148 unigenes had significantly different expression and they were mainly distributed in metabolic and protein synthesis pathways. Additionally, some unigenes controlling anther development were dramatically down-regulated in sterile buds.    Conclusions  These results suggested that an energy deficiency caused by  orf224/atp6  may inhibit a series of genes that regulate pollen development through nuclear-mitochondrial interaction. This results in the sterility of  pol  CMS by leading to the failure of sporogenous cell differentiation. This study may provide assistance for detailed molecular analysis and a better understanding of  pol  CMS in  B. napus.