Methicillin resistant Staphylococcus aureus (MRSA), as one of drug-resistant bacteria, severely affects public health. Rapid and accurate identification of MRSA is essential to prevent the spread of infections and guide effective treatment. Current methods for MRSA detection suffer from the disadvantages of time consuming or sophisticated instrument requirements, which hinder their practical application in resource-limited areas as well as for on-site detection. Herein, we develop a rapid, specific, ultrasensitive colorimetric assay based on the recombinase polymerase amplification (RPA) and magnetic nanoparticles (MNPs) assisted CRISPR/Cas12a for the detection of the mecA gene in MRSA bacteria. This method for detecting mecA gene has a good linear correlation from 1 to 1 * 10<^>6 aM with a low detection limit of 0.2 aM. Furthermore, this method has been successfully applied for detecting mecA gene from the patients infected with MRSA and the results are in good consistence with the culture-based and qPCR-based methods. The developed method can realize the rapid and accurate identification of MRSA within 2 h via the color change observable by naked eye, which is expected to have great prospects in future practical point-of-care testing (POCT) applications for drug-resistant bacteria identification.