To explore the oxidation effects and mechanisms for the oxidation of alkanes by H2O2 in a Fenton system catalyzed by two types of iron bound to soil organic matter (Fe-SOM) in crude oil-contaminated soil, an oxidation experiment was performed in active Fe-SOM and Fe-SOM systems. The results showed that the TPH removal ability of active Fe-SOM (average 0.36 g TPH/g Fe-SOM) was 2.25-fold higher than the corresponding value of Fe-SOM. Active Fe-SOM contained both -NH2 and -OH functional groups, and had a higher content of iron with high binding energy, while Fe-SOM only contained -NH2 groups. Thus, a large yield of hydroxyl radicals (·OH) was generated (8.92 a.u.) by active Fe-SOM catalyzing the decomposition of H2O2, while the corresponding yield of ·OH in the Fe-SOM system was only 4.81 a.u. In addition, the removal efficiency of C17-C23 (70%) was comparable to that of C24-C30 (69%), not restricted by the hydrophobicity of different alkanes. The alkane removal by active Fe-SOM was higher than that by Fe-SOM, although the content of Fe-SOM was double that of active Fe-SOM. In summary, the active Fe-SOM formed in the soil sample containing humic acid-like and hydrophobic acid derivates could catalyze H2O2 decomposition to improve the removal efficiency of crude oil in contaminated soil.