Persulfate (PS)-based advanced oxidation processes (AOPs) for pollutant removal have attracted extensive interest, but some controversies about the identification of reactive species were usually observed. This critical review aims to comprehensively introduce basic concepts and rectify cognitive biases and appeals to pay more attention to experimental details in PS-AOPs, so as to accurately explore reaction mechanisms. The review scientifically summarizes the character, generation, and identification of different reactive species. It then highlights the complexities about the analysis of electron paramagnetic resonance, the uncertainties about the use of probes and scavengers, and the necessities about the determination of scavenger concentration. The importance of the choice of buffer solution, operating mode, terminator, and filter membrane is also emphasized. Finally, we discuss current challenges and future perspectives to alleviate the misinterpretations toward reactive species and reaction mechanisms in PS-AOPs.