Motivated by recent studies that well-documented mineral photocatalyst for bacterial inactivation, a novel natural magnetic sphalerite (NMS) in lead-zinc deposit was first discovered and evaluated for its visible-light-driven (VLD) photocatalytic bactericidal properties. Superior to the reference natural sphalerite (NS), vibrating sampling magnetometeric (VSM) analysis revealed the ferromagnetic property of NMS, indicating its potential for easy separation after use. Under the irradiation of fluorescence tubes, NMS could inactivate 7 log10 Gram-negative Escherichia coli K-12 without any regrowth and metal ions leached out from NMS show no toxicity to cells. The cell destruction process starting from cell wall to intracellular components was verified by TEM. Some products from damaged cells such as aldehydes, ketones and carboxylic acids were identified by FTIR with a decrease of cell wall functional groups. The relative amounts of potassium ion leakage from damaged cells gradually increased from initial 0 to approximately constant concentration of 1000 ppb with increasing reaction time. Superoxide radical (•O2(-)) rather than hydroxyl radical (•OH) was proposed to be the primary reactive oxidative species (ROSs) responsible for E. coli inactivation by use of probes and electron spin resonance (ESR). H2O2 determined by fluorescence method is greatly involved in bacterial inactivation in both nonpartition and partition system. Multiple cycle runs revealed excellent stability of recycled NMS without any significant loss of activity. This study provides a promising natural magnetic photocatalyst for large-scale bacterial inactivation, as NMS is abundant, easily recycled and possessed an excellent VLD bacterial inactivation ability.