Sodium hypochlorite (SHC) is the most commonly utilized carcass and equipment disinfectant in the poultry industry. However, prolonged exposure to SHC can result in the development of bacterial tolerance and exert co-selection on antimicrobial resistance. This study investigated the co-resistance to SHC and multiple antimicrobial agents among Salmonella enterica serovar Indiana (S. Indiana), with a specific focus on the co-occurrence of disinfectant resistance gene qacEΔ1 and the antimicrobial resistance genes (ARGs) revealed by whole genome sequencing (WGS). Additionally, the study examined the transcriptional response of qacEΔ1 and its closely associated ARGs under SHC pressure. Moreover, the study determined the optimal SHC concentration for the decontamination of multidrug-resistant (MDR) S. Indiana on chicken. The results indicated that S. Indiana exhibited a resistance rate of 73.31 % to SHC, and varying levels of resistance to 13 antimicrobial agents. Furthermore, the analysis revealed a significant correlation between the qacEΔ1 gene and ARGs, including catB3, sul1, arr-3 and bla