This study determines the effect of different in situ chemical oxidation (ISCO) technologies on soil microorganisms and total petroleum hydrocarbon (TPH) degradation. Permanganate is a moderate oxidant to the intrinsic microbes while persulfate causes severe bacterial death. TPH removal in the persulfate and permanganate systems is similar, which is higher than that in the hydrogen peroxide system. Permanganate is the most suitable oxidant for ISCO, followed by in situ bioremediation because of its persistence and low toxicity. Chemical oxidation dominates the removal of TPH throughout the experiment in the persulfate systems and during the initial stage in the hydrogen peroxide and permanganate systems. The toxicity of different catalysis/activation methods to in situ microbes decreases in the order: heat> Fe2+/citric acid> Fe2+>no catalysis/activation. If ferrous iron or citric acid is used to catalyze hydrogen peroxide, the pH must be controlled to prevent severe damage to the microbes. There is more dissolved organic carbon in solution in oxidation systems, which shows that the addition of an oxidant increases the solubility and bioavailability of the contaminant. Petroleum degraders are present in the contaminated soil and the addition of oxidants changes indigenous bacterial communities significantly.