Objective The aims of this study were to investigate the antibiotic resistance, disinfectant resistance and their associations in 302 Salmonella enterica Typhimurium (S. Typhimurium) isolates from retail meats, food animals and humans. Methods Antibiotic susceptibility testing was performed according to the Kirby-Bauer disk diffusion method. The minimal inhibitory concentrations (MICs) of disinfectants were determined by broth microdilution method, and disinfectant resistance genes were detected by polymerase chain reaction (PCR) amplification. Results Antibiotic susceptibility testing demonstrated that 96.03% (290/302) of S.Typhimurium isolates were resistant to at least one antibiotic and 79.80% (241/302) were multidrug resistant (MDR). Tested isolates showed the highest resistance to streptomycin (78.81%,238/302), followed by compound sulphonamides (78.15%,236/302), tetracycline (75.50%,228/302) and ampicillin (71.85%,217/302). All isolates were sensitive to cefepime and imipenem. The resistance of S. Typhimurium from food to compound sulphonamides, tetracycline, ampicillin, nalidixic acid, and gentamicin were significantly higher than those from human and animal origin (P<0.05). The resistance of animal isolates to ciprofloxacin and ofloxacin was significantly higher than that of food and human isolates (P<0.05). The resistance of human isolates to cefotaxime and ceftazidime were higher than those of food and animal isolates. The MICs of benzalkonium chloride (BC), triclosan (TCS), trichloroisocyanuric acid (TCCA) and povidone iodine (PVP-I) for S.Typhimurium isolates were 2-64,0.031 25-1,32-1 024 and 256->1 024 mg/L, respectively. In addition, the frequency of resistance to PVP-I, BC and TCS was observed significantly higher in food and animal isolates than human isolates (P<0.05). The qacEΔ1, sugE(p) and qacE disinfectant resistance genes were detected in 56.95% (172/302), 20.53% (62/302) and 2.65% (8/302) of all the isolates, respectively. Notably, qacEΔ1 gene was significantly associated with β-lactam, aminoglycoside, tetracycline, sulfonamide, quinolone and chloramphenicol resistance (P<0.01). Conclusion It was indicated that antibiotic and disinfectant resistance were common among S. Typhimurium isolates and the use of disinfectants or antibiotics may contribute to co-selecting isolates with acquired resistance to other antimicrobials, which could pose significant threats to food safety and public health.