Nsa CMS is a type of cytoplasmic male sterility (CMS) in rapeseed that originated from the cross between Xinjiang wild rapeseed (Sinapis arvensis) and Xiangyou 15 (Brassica napus L.).  Although this CMS variant shows promising applications, the factors contributing to its sterility and their underlying mechanisms remain unclear.  To the best of our knowledge, we successfully assembled and analyzed the mitochondrial genome of 1258A (Nsa CMS) for the first time.  This mitochondrial genome spans 263,010 bp and contains 91 genes, including 33 protein-coding and 36 orf genes.  Our analysis identified a novel mitochondrial gene, orf113b, and a mutated, truncated gene, orf146, both likely linked to the sterility observed in 1258A.  ORF113b and ORF146 were found to impede cell growth, disrupt gene expression associated with complexes I, III, and V of the mitochondrial oxidative phosphorylation pathway, and trigger reactive oxygen species (ROS) production.  In addition, transcriptome data analysis revealed key nuclear genes co-expressed with orf113b and orf146, suggesting that their aberrant expression may be influenced by retrograde signaling from the mitochondria.  This signaling could lead to atypical programmed cell death (PCD) in the tapetum layer, resulting in pollen sterility.  In conclusion, our study not only provides the first characterization of the Nsa CMS mitochondrial genome but also identifies orf113b and orf146 as crucial for pollen sterility.  Furthermore, it suggests that the ROS induced by these mitochondrial genes may play a central role in the abnormal regulation of nuclear genes essential for pollen development, thus offering new insights into the molecular mechanisms underlying Nsa CMS.