Metal-organic framework (MOF) thin films with flexible nature and prominent qualities have opened doors to new technological applications in different fields. Herein, we propose an electrochemical biosensor for the dual detection of Staphylococcus aureus based on the electrodeposition of Cu metal-organic framework (Cu-MOF) thin films. The promising sensing layer with features of good electronic conductivity and enhanced electron-transfer property can not only identify S. aureus through specific micrococcal nucleases in the supernatant but also detect the pathogen directly via aptamer recognition. The dual analysis design ensures the accuracy of this method for S. aureus detection in the range of 7-7 × 106 cfu/mL with the limits of detection of 1.9 and 5.2 cfu/mL. Moreover, the analytical method validation confirmed that the biosensor could efficiently work in complex biological samples, showing good selectivity and specificity and great potential for clinical diagnosis. More importantly, the current proposed strategy is simple and easy to implement without the need for extra signaling elements, which is convenient for timely clinical detection.