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Male sterile line is a useful material for hybridization, but its sterility mechanism, especially proteomic profile, is still not entirely clear. In wheat (Triticum aestivum L.), a male sterile Bainong (BNS) genotype whose sterility could be manipulated by temperature was recently selected. We focused on the proteomic profile change of anthers from the male sterile line (SL) and its conversional line (CL). Two-dimensional gel electrophoresis and MALDI-TOF-MS technologies were utilized for proteomic profiles analysis. Differently abundant protein spots (over 2-fold, P < 0.05) were selected for identification analysis. Compared to CL, 24 up-regulated and 23 down-regulated proteins were identified in SL. Protein metabolism-related proteins, which included a ubiquitin-conjugating enzyme E2 (23 kDa) and an ATP-dependent Clp protease proteolytic subunit, were over-accumulated in SL anthers. Alcohol dehydrogenase ADH1A, fructose-bisphosphate aldolase, chloroplast fructose-bisphosphate aldolase, and NADP-dependent malic enzyme were notably down-regulated in SL anthers. Up-regulated prohibitin protein Wph and a translationallycontrolled tumor protein homolog, and down-regulated histone acetyltransferases HAT1 and HAT2, and DNA directed RNA polymerase subunit α were identified in SL anthers. These dramatically changed proteins may play a crucial role in abnormal anther development and pollen abortion in BNS.