Proteomics is one of the main contents of functional genomics era, and plays an important role in understanding gene function, molecular mechanisms, etc. Plant proteomics, which is regarded as a branch of proteomics, has been applied and investigated more and more extensively, especially in exploring how plants and pathogens recognize each other and differentiate to establish either a compatible or an incompatible relationship. This review have summarized the proteomic studies on plant-pathogen interactions from both the plant and pathogen view points in recent years, particularly focused on plant response to fungi, viruses and bacteria infection. Finally, the prospects are forecasted to provide some references and theoretical basis for further study.