The increased release of various emerging organic contaminants into natural waters has posed great threats to ecological safety and public health. The ensuing global water contamination has necessitated the development of highly efficient treatment strategies for water purification. Herein, we presented for the first time that the combined utilization of permanganate (Mn(VII)) and periodate (PI) could synergistically and rapidly accomplish complete destruction of different organic micropollutants (e.g., bisphenol F, methotrexate, and tetracycline) within 2–5 min. Comparatively, the single treatment only eliminated very small amounts of micropollutants. Mechanistic investigations were performed using the trapper-based electron spin resonance, scavenging and probe experiments, UV–vis spectra analysis, determination of iodine species, and multiple validation tests. These data collectively suggested that the highly reactive Mn(V)/Mn(VI) intermediates played the leading role in accelerating contaminant abatement within the Mn(VII)/PI oxidation system. Reactive oxygen/or iodine species (1O2, OH, O2-, IO3, and IO4) and low valence Mn species (Mn(II), Mn(III), and in-situ formed MnO2 colloids) did not participate in decontamination in this process. Subsequently, the oxidized products of three micropollutants were determined, and the transformation pathways were clarified. Ring-opening, C-C bond cleavage, demethylation, carbonylation, and hydroxylation reactions mainly occurred in the degradation process. Notably, the combined system did not yield any toxic iodinated end products. Finally, the environmental risks of the degradation products were also evaluated based on in silico QSAR-based prediction tools. Overall, this study provides a novel, highly efficient, and green treatment technology, i.e., Mn(VII)/PI system, which could be employed for rapid and sustainable water decontamination.