Salt stress is a critical factor of abiotic stress in agricultural production that significantly affects seed germination and early seedling development. In this study, we characterized the function of the Arabidopsis Long Hypocotyl 2(HY2) gene in NaCl signaling. The hy2 mutant was NaCl-insensitive, whereas HY2-overexpressing lines shows NaCl-hypersensitive phenotypes during seed germination. Induced by exogenous NaCl, the transcription and the protein level of HY2 were up regulated, and HY2 positively mediated the expression of downstream stress-related genes of RD29A, RD29B and DREB2A. With further quantitative proteomics, we got the patterns of 7,391 proteins under salt stress, and identified 215 differentially regulated proteins (DRPs) specifically regulated by HY2. According to GO enrichment analysis, these proteins are mainly involved in ion homeostasis, hormone response, reactive oxygen species(ROS) metabolic, photosynthesis and detoxification pathway to response salt stress . These results direct the pathway of HY2 participating salt stress, and provide new insights for the plant to resist salt stress.