Viable But Nonculturable (VBNC) Bacteria, which represent a unique population of microorganisms in drinking water systems, have become a potential threat to human health. Current studies on VBNC cells usually fail to obtain pure VBNC state bacteria, which may lead to inaccurate results. We therefore introduce a novel method of VBNC cell separation and purification in this paper. PAH-coated magnetic nanoparticles (MNPs) were synthesized and found to be capable of capturing and releasing bacterial cells with high efficiency. With the aid of an additional incubation step, VBNC cells were easily isolated and purified from normal bacteria using functional MNPs. Our method represents a new technique that can be utilized in studies of VBNCs.