Objective To analyze the impact of microbial detection technology on food inspection results. Method 100 samples of food to be tested from a testing institution between January 2023 and December 2023 were selected as the research subjects, all of which underwent fluorescence PCR and traditional national standard methods. The microbiological testing techniques were observed and recorded in the food inspection results. Result Among the 100 food samples to be tested, 52 were fruits, 34 were vegetables, and 14 were meat. Among the 10 food samples sampled, 4 were Escherichia coli, followed by 3 Staphylococcus aureus and 2 were Salmonella. According to the traditional national standard method, 4 were Escherichia coli, and 3 were Salmonella and Staphylococcus aureus; Among the 100 food samples from 3 categories, the highest contamination rates were found in raw animal meat, raw poultry meat, and aquatic products. A total of 17 samples were contaminated, and the most pathogenic bacteria detected were Escherichia coli, Staphylococcus aureus, and Salmonella. Conclusion Microbial detection technology can detect pathogenic microorganisms in food, distinguish specific types, and has good application value.