Listeria monocytogenes poses a major global food safety concern as a widespread pathogen causing listeriosis. In this study, a total of 553 L. monocytogenes isolates across 9 food types sampled during 2020-2023 in Shanghai, the largest city in China, and among the largest metropolitan areas worldwide, were identified using whole-genome sequencing (WGS). The association among clonal complexes (CCs) and food matrices was determined using an Apriori algorithm approach. Results revealed that less virulent CC9 and CC121 isolates without LIPI-2-4 were the predominant strains frequently detected, showing strong association with pork, beef, lamb, chicken, and processed meat products, suggesting their widespread presence in various meat types. Virulent CC8 without LIPI-2-4 was predominantly found in processed meat products, cooked meat products, and clinical cases. More virulent CC87 with LIPI-4 was frequently detected in clinical cases and chicken. Similarly, CC2 with LIPI-3 showed a strong association with seafood products. Therefore, the observed CCs aligned with previously defined virulence classes, offering valuable data for microbiological risk assessment. Further research is necessary to explore unique CCs in China and the virulence profiles. Nevertheless, this study highlights the insufficiency of relying solely on LIPI-1-4 for determining L. monocytogenes pathogenicity. Notably, the presence of inlA PMSC mutations revealed the distribution of virulence potential of L. monocytogenes, which might be helpful to improve risk assessment approaches. Furthermore, incorporating CCs into L. monocytogenes surveillance may aid in tracing contamination sources and monitoring transmission patterns, offering insights for risk assessment.