In present investigation, we studied how mitochondrial–nuclear interactions may give rise to the third abnormal whorl floral organ in cytoplasmic male sterility (CMS) stem mustard, which exhibited complete conversion of homeotic transformations of stamens into other floral organ structures. In this system, expressions of AP3-like, PI-like and AG-like genes, the counterpart of the Arabidopsis nuclear ABC model genes related to floral organ development, were specifically altered in floral organs of CMS plants. When mitochondrial-specific inhibitor was applied to wild type fertile stem mustard plants, expressions of AP3-like, PI-like and AG-like genes were repressed. As a consequence, abnormal floral organs were observed in its maintainer line treated with mitochondrial-specific inhibitor. Thereby, we suggest that nuclear MADS-box transcription factors subject to mitochondrial retrograde regulation were associated with cytoplasmic homeosis in CMS stem mustard and could be mimicked by specifically inhibiting mtETC.