For commercially viable direct methanol fuel cells, electrocatalysts play a crucial role in motivating the sluggish methanol oxidation reaction (MOR) over anode. Unfortunately, the large-scale applications of current MOR catalysts are hampered by their poor tolerance to poisoning and fast activity degradation. Herein, a unique composite catalyst comprised of partial Pd nanoparticles and partial Pd single atoms (PdNPs/Pd-Nx@C) is developed. The as-fabricated catalyst exhibits remarkable activity of 9.45 mA·cm−2 towards MOR in alkaline solution, which is 7.05 and 3.92 times that of commercial Pd/C and nanoparticle type (PdNPs@C) electrocatalysts, respectively. Impressively, the PdNPs/Pd-Nx@C shows the highest long-time stability with 90.38% and 89.8% of the initial activity retained after 3600 s chronoamperometry (CA) test and 2000 cycles of cyclic voltammetry (CV) measurements with accelerated durability test (ADT), respectively. Combined with high-angle annular darkfield scanning transmission electron microscopy (HAADF-STEM), X-ray adsorption fine structure (XAFS) spectra and X-ray photoelectron spectroscopy (XPS) analyses, the superior performance of PdNPs/Pd-Nx@C can be ascribed to the synergistic effect from the Pd single atoms, N-doped carbon supports and Pd nanoparticles. Notably, the embedded Pd single atoms are liable to transfer electrons to the substrate due to the electronic metal-support interactions (EMSI) and the charge transfer between Pd nanoparticles and carbon supports is suppressed, inducing a weak adsorption strength of poisonous carbonous intermediate species on active Pd nanoparticles and improved poisoning tolerance in MOR process, which is verified by density functional theory (DFT) calculations as well as CO-stripping voltammetry experiments. This work not only contributes the first example of a synergistic catalyst between nanoparticles and single atoms for MOR but also deepens the knowledge on the metal-support interaction.