The synthesis of shape-, facet-, and composition-controlled Pd-based nanocrystals and the study of their catalytic reaction mechanisms are significant to and challenging for the development of advanced catalysts applicable to direct liquid-fuel cells (DLFCs). In the present study, we prepared (100)-faceted β-PdH cubes and (111)-faceted β-PdH octahedra, which offered the opportunity to investigate the link between catalytic performance and the shape/facet/composition of nanocrystals. The β-PdH cubes and octahedra remarkably boosted catalytic activity and stability to the formic acid/methanol oxidation reaction (FAOR/MOR), due to the ligand effect originating from the interstitial alloying of β-PdH. Notably in this regard, β-PdH cubes exhibited the highest FAOR/MOR activity among Pd-based catalysts, owing to the relatively high CO tolerance on the Pd(100) facets. Our results confirm that simultaneous control of ligand and facet effects is an effective approach to the design of catalysts suitable for liquid fuel oxidation electrocatalysis.