Objective In order to explore the contamination and drug resistance of foodborne pathogens in fresh cut fruits and vegetables, samples were collected from retail markets in five district in Beijing. Methods The national standard method of food microbiological examination was used to detect Staphylococcus aureus, Salmonella, Listeria monocytogenes and Escherichia coli respectively. The drug resistance of the isolates was determined, and the Diarrheagenic Escherichia coli was screened by fluorescent PCR. Results Among 326 fresh cut fruits and vegetables sold in Beijing, the contamination rates of Staphylococcus aureus, Listeria monocytogenes, Salmonella, Escherichia coli and Enteroaggregative Escherichia coli were 15.34%, 1.84%, 0%, 9.51% and 1.23% respectively. 50 strains of Staphylococcus aureus isolated in this study were mainly resistant to penicillin (90.00%) and oxacillin (48.00%), 31 strains of Escherichia coli were mainly resistant to compound sulfamethoxazole (67.74%) and ampicillin (64.50%), and 4 strains of Enteroaggregative Escherichia coli showed multiple drug resistance. All 6 strains of Listeria monocytogenes were sensitive to 10 kinds of antibiotics. Conclusion This research provided a scientific experimental basis for formulating the prevention and control strategy of foodborne diseases.