Nonalcoholic fatty liver disease (NAFLD) is a common chronic liver disease with an increasing morbidity. However, its pathogenesis is still elusive and its diagnosis and treatment need to be improved. The emergence of proteomics has pushed NAFLD research forward and twenty-one associated studies have been reported by now. Recent progress in proteomic techniques allows evaluation of molecular changes associated with disease, thereby permitting to identify novel biomarkers and therapeutic targets. Herein, the application of proteomics in the study of the diagnosis, pathogenesis and other related fields of NAFLD were comprehensively reviewed. Firstly, empirical knowledge about categories of subjects and samples, experimental methods and biomarker selection was summarized. Secondly, in addition to studies utilizing proteomics to explore roles of etiological factors, risk factors and important molecules in the pathogenesis of NAFLD, studies of NAFLD pathogenesis by the means of subcellular proteomics, modification-specific proteomics, and the integration of proteomics and transcriptomics were also shown. Thirdly, methods for analyzing differentially expressed proteins and implications of these results were highlighted. It's hoped that this review can help to promote the application of proteomics in exploring disease pathogenesis and discovering novel biomarkers and treatment targets.