Copper-containing ZSM-5 zeolite can facilitate the direct oxidation of methane to form methanol under mild condition with high selectivity. However, due to the limitation of the experimental characterization, the identification of the catalytic sites in Cu-exchanged zeolites still remains unclear. Herein, the reactivity of different [CuxOy] (x = 1, 2, 3; y = 1, 2, 3)- and [CuOH](+)-ZSM-5 active sites towards methane partial oxidation process has been elucidated by using density functional theory (DFT) calculations. It is indicated that i) C-H activation over five different active sites obeys the radical mechanism, and the reactivity follows the sequence: copper-oxyl [CuO](+) (S = 1) > tricopper [Cu3O3](2+) (S = 3/2) > bis-(mu-oxo)-dicopper [Cu2O2](2+) (S = 1) > mono-(mu-oxo)-dicopper [CuOCu](2+) (S = 1) > mono-copper [CuOH](1)(+) (S = 1/2); ii) The rate constants for C-H bond cleavage of methane at the reaction temperature are faster at the higher temperature; iii) The descriptors for C-H activation of methane on [CuxOy] (x = 1(similar to)3, y = 1 3)- and [CuOH](+)-ZSM-5 have been established, for which the active site with more spin density and less negative charge will induce the lower activation barriers for C-H activation of methane. Meanwhile, the stronger hydrogen affinity of the active site is, the lower the activation barriers of methane C-H activation will be. Taken the stability and activation barrier together, the catalytic performance of copper-oxyl site has been enhanced by the presence of water.