We integrate recombinase polymerase amplification (RPA) with CRISPR/Cas9-initiated nicking rolling circle amplification (CRISPR/Cas9-nRCA) for detecting Staphylococcus aureus. This approach utilizes a unique dimeric G-triplex structure, demonstrating firstly enhanced ThT fluorescence for target detection. The proof-of-concept study introduces a new avenue for integrating isothermal amplifications with CRISPR/Cas9 in the fields of pathogen detection and disease diagnosis.