Natranaerobius thermophilus is a unique extremophile, which exhibits high adaptability and preferability to the combined extreme conditions of high salt concentration, alkaline pH and elevated temperature. At present, the global regulation of genes and proteins in the salinity adaptation strategies of N. thermophilus remains unclear. In this study, we employed the isobaric tags for relative and absolute quantification (iTRAQ) method to investigate the protein abundances of N. thermophilus in response to different Na+ concentrations (2.5 M, 3.1 M, 3.7 M, 4.3 M) at high alkali (pH55°C9.5) and high temperature (53℃). In addition, the transcriptional expression level of some differentially expressed proteins, the expression pattern clustering, and the protein-protein interaction network were analyzed. A total of 1490 proteins were identified, and 659 proteins displayed significant expression under 3.1M (HS3.1 group), 3.7M (HS3.7 group), and 4.3M (HS4.3 group) Na+ concentrations compared with the 2.5M Na+ concentrations (CK2.5 group). Of them, 59 showed simultaneously higher expression and 91 showed simultaneously lower expression. Both GO, COG and KEGG enrichment analysis revealed that up-regulate expressed genes were enriched in membrane transporters, amino acid transport and metabolism, catalytic activity, the TCA cycle, detoxification and stress response and metabolic pathways. Among them, 59 upregulated simultaneously proteins were analyzed and confirmed at the gene expression level by Droplet Digital PCR (ddPCR). Based on our results, we propose that under extremely high salinity pressure，cell membrane high activity, increased biosynthesis and transportation of osmotic protectants, and increased energy production and conversion contribute to the Salt stress tolerance of N. thermophilus. The aim of this study was to provide new insight into the response of N. thermophilus to high-salt at alkaline pH and elevated temperature and identify mechanisms responsible for this adaptation.