Sepsis, the systemic response to infection, is a life-threatening situation for patients and leads to high mortality, especially when caused by antimicrobial resistant pathogens. Prompt diagnosis and identification of the pathogenic bacteria, including their antibiotic resistance, are highly desired to yield a timely decision for treatment. Here, we aim to develop a platform for rapid isolation and efficient identification of Staphylococcus aureus, the most frequently occurring pathogen in sepsis. A peptide (VPHNPGLISLQG, SA5-1), specifically binding to S. aureus, was conjugated to the PEGylated magnetic nanoclusters, successfully enabling the specific capture and enrichment of S. aureus from blood serum. Consequently, fast detection of the antimicrobial resistance of the collected S. aureus was achieved within 30 min using a novel luminescent probe. These magnetic nanoclusters manifest a promising diagnostic prospect to combat sepsis.