The sterile line of common wheat (Triticum aestivum) with the cytoplasm of Ae. ventricosa is Ven cytoplastmic male sterile (Ven CMS), and it is one type of S^v CMS in wheat. To better understand the molecular mechanism on nucleuscytoplasmic interaction male sterility in wheat, we analyzed differential proteomics at uninucleate and binucleate stages in sterile line JI5418A and its maintainer line JI5418B. Another proteins were separated by two dimensional electrophoresis. Differential protein spots were identified by matrixassisted laser desorption /ionization tandem timeofflight mass spectrometry (MALDITOFTOF). Identification and function annotation and analysis of these proteins were analyzed by bioinformatics methods. About 2000 reproducibly protein spots could be visualized on these 2Dgels within M 19.0-100.0 kD and pI 47. Ninety eight differentially expressed proteins were found between JI5418A and JI5418B, and among these proteins 56 showed same differences at both stages. Forty one proteins were successfully identified in NCBI database. Eighteen and 23 proteins were significantly downregulated expressed in JI5418A, and JI5418B, respectively. The differentially expressed proteins involving in energy metabolism, active oxygen scavenge, ribosome synthesis and pollen wall formation existed in both sterile and fertile lines. GO analysis predicted many differential expressed proteins involved in electron transport and energy metabolism, ribosome metabolism, and active oxygen metabolism, etc. in biological process, distributed in membrane region and mitochondria in cellular component, DNA and RNA binding function and hydrolytic enzymes in molecular function. KEGG pathways analysis indicated that more proteins involved in carbohydrate metabolism, active oxygen metabolism and protein assembly and folding than other pass ways. It is speculated that male sterility in JI5418B might be related to energy metabolism, active oxygen scavenging process. Ribosomal protein and chaperone protein also have great roles in controlling its fertility. Male sterility in Ven CMS might be related to the regulation disorders in protein processing and material synthesis.