Viable but non-culturable (VBNC) bacteria after chlorination disinfection pose a considerable threat to the public health and environment. The current work aimed to uncover the stress adaptation mechanisms of VBNC Salmonella Enteritidis to sodium hypochlorite. In this study, we investigated the morphology, gene expressions and proteomic profile in VBNC S. Enteritidis. It demonstrated that 109 cells/mL of bacteria could transition into the VBNC state after exposure to 50 mg/L chlorine for 2.5 h. The VBNC state cells exhibited cellular membrane impairment, decreased size, and intracellular ATP depletion compared to the culturable cells. In the VBNC state cells, there was a significant increase in intracellular reactive oxygen species (ROS) levels and NAD+/NADH ratios. This observation suggested an imbalance in the intracellular redox status of the VBNC bacteria. Transcriptome and proteomic analysis revealed significant upregulation of the resistance-nodulation-division (RND) efflux systems (arcA, tolC, ramA), oxidative stress response genes (soxR, trxA, grxB), DNA repair genes (lexA, radA, mutH, mutL), and virulence factor genes (sseA, sseL, eutS, and eutE). Our findings indicated that it is important to formulate disinfection protocols that are specifically designed for food processing plants and healthcare facilities, focusing on implementing a more thorough disinfection method to effectively eradicate VBNC cells.