Objective To develop a rapid method for the screening and identification of foodborne （C. perfringens） isolates using multiple nucleic acid detection system combined with matrix assisted laser desorpt ionionization time of flight mass spectrometry （MALDI-TOF MS）， and to provide a new strategy for the identification of foodborne pathogens.Methods Samples from a food poisoning incident in Zhangjiagang City were collected for rapid screening with the multiplex nucleic acid detection system and MALDI-TOF MS， detection with traditional biochemical and MALDI-TOF MS， the accuracy of the results was verified by Real-time PCR combined with 16S rRNA sequencing.Results After initial screening using a multiplex nucleic acid detection system and MALDI-TOF MS， preliminary evidence indicated the samples had C. perfringens. Following GB 4789.13—2012 testing protocol， 31 strains of C. perfringens were identified in 122 samples associated with food poisoning incidents. Furthermore， fluorescence quantitative PCR and 16S rRNA gene sequencing were employed to verify 7 strains that showed inconsistent biochemical test results. These additional analyses ultimately confirmed that these 7 strains were indeed C. perfringens.Conclusion The multiple nucleic acid detection system has the advantages of prompt detection and elimination of routine detection items， and the MALDI-TOF MS is easy to operate， rapid， has a high accuracy of detection results. The combination of the two technologies can quickly and accurately screen and confirm pathogenic factors， providing a new effective method for the detection of foodborne pathogens.