Atomically ordered intermetallic nanoparticles (iNPs) have sparked considerable interest in fuel cell applications by virtue of their exceptional electronic and structural properties. However, the synthesis of small iNPs in a controllable manner remains a formidable challenge because of the high temperature generally required in the formation of intermetallic phases. Here we report a general method for the synthesis of PtZn iNPs (3.2 ± 0.4 nm) on multiwalled carbon nanotubes (MWNT) via a facile and capping agent free strategy using a sacrificial mesoporous silica (mSiO2) shell. The as-prepared PtZn iNPs exhibited ca. 10 times higher mass activity in both acidic and basic solution toward the methanol oxidation reaction (MOR) compared to larger PtZn iNPs synthesized on MWNT without the mSiO2 shell. Density functional theory (DFT) calculations predict that PtZn systems go through a “non-CO” pathway for MOR because of the stabilization of the OH* intermediate by Zn atoms, while a pure Pt system forms highly stable COH* and CO* intermediates, leading to catalyst deactivation. Experimental studies on the origin of the backward oxidation peak of MOR coincide well with DFT predictions. Moreover, the calculations demonstrate that MOR on smaller PtZn iNPs is energetically more favorable than larger iNPs, due to their high density of corner sites and lower-lying energetic pathway. Therefore, smaller PtZn iNPs not only increase the number but also enhance the activity of the active sites in MOR compared with larger ones. This work opens a new avenue for the synthesis of small iNPs with more undercoordinated and enhanced active sites for fuel cell applications.