A novel magnetic natural pyrrhotite (NP) mineral photocatalyst was developed and modified by thermal treatment. Their photocatalytic activity were evaluated by photocatalytic inactivation of Escherichia coli K-12 under visible light. As compared to NP, the annealed NP was found to exhibit a remarkable enhanced bactericidal activity. Among them, the NP treated at 600 °C in air (NP600) had the highest activity and the inactivation rate was nearly 3 times higher than that of untreated NP. The X-ray diffraction (XRD) spectra indicated the mineral phase of NP600 transformed to mixed crystallite phases of hematite-pyrite (Fe2O3–FeS2) composite. Thus, the enhanced photocatalytic performance was mainly attributed to the formation of Z-scheme photocatalysis system composed of hematite and pyrite, which could improve the electron-hole separation efficiency and the bactericidal efficiency. Scavenger study demonstrated that the dominant bactericidal agent changed from superoxide radical (radical dotO2−) for NP to hydroxyl radical (radical dotOH) for NP600. Moreover, vibrating sampling magnetizer (VSM) analysis revealed that the saturated magnetism of NP after thermal anneal was enhanced. The strong magnetic behavior of thermal treated NP enabled the magnetic recovery of photocatalysts after liquid phase reaction. In addition, NP600 was more stable than untreated NP and with lower metal ion leakage even after four reaction cycles. This work supplied a cost-effective natural mineral-based photocatalyst and an efficient modification strategy to extend the application field of natural minerals in water disinfection.