The most common odor substance found in surface water is 2-methylisoborneol (2-MIB), and this substance cannot be effectively removed by conventional water treatment processes. Persulfate (S2O82-, PS)-based oxidation has recently received wide attention due to its promising ability to remove refractory pollutants. In this research, the degradation of 2-MIB by PS activated with iron (II) (PS-Fe2+) or heat (PS-Heat) was investigated. Kinetic analysis indicated that 2-MIB degradation in both of the systems (PS-Heat and PS-Fe2+) followed a pseudo-first-order reaction. For the PS-Heat system, a high temperature, a high PS initial concentration and weakly acidic conditions benefit the degradation of 2-MIB. Coexisting anions inhibit 2-MIB removal in the following order: CO32- > HCO3- > Cl-. For the PS-Fe2+ system, the optimum molar ratio of PS to Fe2+ ([PS]: [Fe2+]) was 1:1. The 2-MIB degradation rate increased under acidic conditions and with the addition of citrate; however, the rate decreased with an excess Fe2+ dosage. In addition, this study was the first to examine the behavior pattern of algal photosynthesis activity as well as the total and extracellular 2-MIB of Pseudoanabaena sp. (a typical 2-MIB-producing cyanobacterium) in the PS-Fe2+ system. Moreover, a comparison study of the removal of 2-MIB in actual algae-containing water under the oxidation of PS-Fe2+, potassium permanganate (KMnO4), and sodium hypochlorite (NaClO) was firstly carried out. The results provide useful theoretical and engineering information for treating algae-loaded water.