Objective To identify the suspicious food, pathogenic factors, and risk factors of a foodborne disease outbreak in a middle school in Nanjing, and to discuss the problems found during the investigation, providing a basis for the prevention, control, and investigation of similar incidents in the future. Methods A comprehensive methodology integrating field epidemiological analysis, hygiene investigation, and laboratory testing was employed. Field epidemiological investigations identified the suspected meal and food items, hygiene surveys pinpointed the contamination points, and laboratory testing confirmed the pathogenic agent. Various samples were collected for PCR-based multi-pathogen screening. Samples positive for?Clostridium perfringens?nucleic acid underwent bacterial isolation and anaerobic culture, followed by whole-genome sequencing, virulence gene detection, and homology analysis of the isolated strains. Results 56 suspected cases were identified, with clinical symptoms mainly including diarrhea (100%) and abdominal pain (100%), and a few cases exhibiting nausea and vomiting. The epidemic curve exhibited a point source exposure pattern, with an incubation period ranging from 2 to 14 hours. Analytical epidemiological investigation identified the "bok choy" served for dinner on August 14 as the suspected exposure source.Clostridium perfringens was detected in 30 anal swab samples, one food sample (Chinese cabbage), and one environmental sample. Specifically, the concentration of Clostridium perfringens in the dinner sample of Chinese cabbage on the 14th day was 3.2×105 CFU/g. Whole-genome sequencing revealed that isolates from 10 cases, 8 employees, and one food sample (Chinese cabbage) all belonged to the ST734 Lineage 1 clade, with positive CPE virulence genes. The number of core genome SNP differences ranged from 0 to 2, indicating high homology. Conclusion Through on-site investigation and traceback analysis, it was determined that this incident was an outbreak of foodborne illness caused by consuming "Chinese cabbage" served for dinner on August 14th in the school cafeteria. The causative agent was Clostridium perfringens. The new technology of whole-genome sequencing can play a precise role in tracing the source of foodborne disease outbreaks.