Pt is widely used as the catalyst for methanol oxidation reaction (MOR) in direct methanol fuel cells (DMFC). However, the high cost and limited supply of pure Pt limit the commercialization of DMFC. Herein, MOR catalyzed by variously designed Pd-doped PtmPdn was studied with the density functional theory (DFT); the PtmPdn(111) surface was chosen since it is the most stable surface among various low-index surfaces. The hydrogens in methyl groups were priorly dehydrogenated on Pt(111), followed by hydrogen in the hydroxyl group. The effects of both the ratio of Pt:Pd and the type of the alloy on the activity of PtmPdn catalysts toward MOR were also studied; both ordered and disordered PtPd with the 1:1 ratio had better catalytic activity towards MOR than other catalysts. Specifically, the disordered Pt:Pdd with the Pt:Pd ratio of 1:1 had the best activity for the relatively stronger adsorption of COH, but the lowest binding with CO and a moderate d band center. The adsorptions of both COH and CO are key steps in the MOR, since the steps of CH3OH→CH2OH→CHOH→COH have downhill energy profiles, while COH→CO is an uphill reaction. In addition, the d band centers of the surface atoms move towards the Fermi level with the increase of the Pd content; the d band can also be tuned by changing the atom arrangement. These findings can be used as rules to design high-performance catalysts for MOR.