As non-precious catalysts, Ni-based catalysts play a significant role in methanol oxidation for energy conversion technologies. At the same time, the effect of the complicated chemical environment on catalytic efficiency remains unclear. Here, the coordination environment of Ni active sites in spinel nickel-manganese (NiMn2O4 and MnNi2O4) is investigated as a platform to elucidate the correlation with catalytic performance in methanol electro-oxidation. The occupation of Ni2+ ions in these structures modulates the intrinsic activity of Ni active sites in NiMn spinels, resulting in different catalytic mechanisms and intrinsic active sites efficiency, although they have similar morphology and structure. The high-symmetry NiO6 octahedral structure in inverse spinel MnNi2O4 exhibits superior catalytic performance and stability compared to the NiO4 tetrahedral structure in normal NiMn2O4 spinel. Specifically, at 1.50 V vs. RHE, the MnNi2O4 inverse spinel delivers mass activity and specific activity for methanol oxidation that are 1.9 and 3.5 times those of the normal NiMn2O4 spinel, respectively. Furthermore, it also maintains a stable current density of 33.5 mA cm2 at 1.56 V vs. RHE for 25 hours. Theoretical calculations reveal that Ni sites in MnNi2O4 exhibit a significantly lower activation energy barrier and enhanced CO anti-poisoning capability compared to those in NiMn2O4. The Ni site-dependent coordination environment in spinel structures provides useful insights into catalyst development and the methanol oxidation mechanism.