Multidrug‐resistant (MDR) bacterial infections constitute a major public health problem worldwide. A rapid method for the detection of methicillin‐resistant Staphylococcus aureus (MRSA) is critical for the timely prevention of bacterial infections and the accurate clinical use of drugs. The nuc and mecA genes are potentially indicative of MRSA infection and in this study, a multiplex molecular fluorescence multi‐enzyme isothermal rapid amplification visual assay was proposed and established. The method is capable of detecting MRSA at 17 min, 40°C amplification, and is well differentiated from common clinical bacteria in specific assays, with 500 colony‐forming units (CFU) mL−1 of MRSA detected under optimal conditions. This method has excellent diagnostic capabilities versus classical methods to detect clinical samples and shows potential in the identification of pathogenic microorganisms in a clinical setting.