Wastewater treatment plants (WWTPs) are considered important reservoirs of antibiotic resistance genes (ARGs) and function as the main sources of ARGs in the environment. Membrane bioreactors (MBRs) have been recognized as effective tools for removing ARGs in WWTPs.There are a large number of pathogens and resistance genes in colloids, particulate matter, suspended matter, and microbial metabolites in intercepted wastewater by MBR. However, the distribution characteristics of resistance genes in membrane cleaning sludge remains unclear. In this study, resistance genes of membrane cleaning sludge were analyzed using a metagenomic technique. The results showed that there were 39 phyla in the membrane cleaning sludge. Proteobacteria, Nitrospirae, and Actinobacteria were the dominant phyla. The dominant genera were Nitrospira, Pseudomonas, and Bradyrhizobium. The pathogens accounted for 10.54% of all bacteria in the sample, among which Pseudomonas had the highest abundance, accounting for 3.94%. A total of 17 types of antibiotic resistance genes and 16 types of metal resistance genes (MRGs) (15 types of single metal resistance genes and 1 types of multi-heavy metal resistance gene) were identified. Multidrug resistance genes had the highest abundance, accounting for 49.08%. Multi-heavy metal resistance genes were the most abundant, accounting for 34.58%. The copper resistance genes were the most abundant of the single metal resistance genes, accounting for 19.99%. The most important functional pathway of microbial community in the membrane cleaning sludge was metabolic related, and many genes identified were related to human diseases. The numbers of genes related to bacterial resistance and bacterial infectious diseases were the largest, accounting for 34.50% and 16.62%, respectively. These results indicate that there were abundant ARGs, MRGs, and pathogens in the membrane cleaning sludge, which has potential environmental health risks. It is necessary to strengthen the control of ARGs, MRGs, and pathogens in membrane cleaning sludge to provide guidance for selecting appropriate technologies for effectively removing ARGs, MRGs, and pathogens.