Homogeneous catalytic oxidations of cyclohexene by transition‐metal‐substituted phosphotungstates [PW11M(L)O39]m− (PW11M, M=CoII, CuII, FeIII, NiII, MnII, L=H2O or absence) with hydrogen peroxide in acetonitrile were experimentally studied. The catalytic activities of allylic oxidation were found to strongly depend on the transition metals, and PW11Co showed the highest activity. The product distribution and the catalyst stability were dominated by mole ratio of hydrogen peroxide to PW11M, whereby low or high mole ratios led to stable structure of PW11M and predominant formation of allylic oxidation products or decomposition of PW11M, respectively. Different from the activation of the allylic C−H bond by radicals, the oxidation of C=C double bond was based on tungsten‐peroxo species. A reaction mechanism composed of radical and nonradical processes was proposed from NMR, EPR, and kinetic data, to describe the reaction pathways of cyclohexene oxidation.