Objectives: To further elucidate the molecular mechanism of cytoplasmic male sterility(CMS)in soybean,a differentialproteomic analysis was completed between the CMS line NJCMS1A and its maintainer NJCMS1B using iTRAQbasedstrategy.Results:As a result,180 differential abundance proteins(DAPs)were identified,of which,60 weredown-regulated and 120 were up-regulated in NJCMS1A compared with NJCMS1B.Bioinformatic analysisshowed that 167 DAPs were annotated in 41 Gene Ontology functional groups,106 DAPs were classified into20 clusters of orthologous groups of protein categories,and 128 DAPs were enrichment in 53 KEGG pathways.Fifteen differential level proteins/genes with the same expression pattern were identified in the further conjointanalysis of DAPs and the previously reported differential expression genes.Moreover,multiple reaction monitoringtest,qRT-PCR analysis and enzyme activity assay validated that the iTRAQ results were reliable.Conclusions: Based onfunctional analysis of DAPs,we concluded that male sterility in NJCMS1A might be related to insufficiencies inenergy supply,unbalance of protein synthesis and degradation,disruption of flavonoid synthesis,programmedcell death,abnormalities of substance metabolism,etc.These results might facilitate our understanding of themolecular mechanisms behind CMS in soybean.