Objective Understanding of bacterial antibiotic resistance is the basis for guiding clinical anti-infective therapy and monitoring antimicrobial resistance trends. The study was aimed to investigate the antibiotic resistance characteristics of nontyphoidal Salmonella isolates from foodborne disease cases in Jiangxi Province in 2018, study the correlations between resistance phenotypes and genotypes, and evaluate the application prospects of whole genome sequencing (WGS) in antimicrobial resistance surveillance. Methods In this study, 58 nontyphoidal Salmonella strains were isolated from foodborne disease patients in Jiangxi Province in 2018 and were tested for susceptibility to 14 antimicrobials using broth microdilution. The 58 isolates were subjected to WGS, and resistance genes were identified from assembled sequences that compared with ResFinder database. Results 77.59%(45/58)of isolates were resistant to tetracycline, and 72.41%(42/58) were resistant to ampicillin. 100.00% of isolates were susceptible to imipenem. 56.90%(33/58) of isolates displayed resistance to at least 3 classes of antibiotics, and 3.45%(2/58) of isolates had resistance to at least 6 of 8 classes tested. A total of 47 unique resistance genes referred to 11 classes of antibiotics, plus mutations in gyrA, gyrB and parC structural of quinolone resistance-determining region(QRDR), were identified. 100.00%(58/58) of isolates had aminoglycoside resistance genes, and 72.41%(42/58) of isolates harboured tetracycline resistance genes. Macrolide resistance genes were presented in 3.45%(2/58) of isolates. 77.59%(45/58) of isolates were contained at least 3 classes of antibiotics resistance genes, and 1.72%(1/58) of isolates harboured at least 9 classes of resistance genes. The overall resistance genotypes and phenotypes were consistent in 93.43%(611/654) of cases. Except quinolones, the correlations were above 91% for tested antibiotics. Correlations were 100% for some classes of antibiotics. Conclusion The antibiotic resistance phenomenon of these isolates was serious. The resistance phenotypes were in good accordance with genotypes, and WGS can be used as an effective tool to predict the antibiotic resistance of nontyphoidal Salmonella. As more new antibiotic resistance genes were discovered, the consistency of resistance genotypes and phenotypes will be further improved.