Tailoring the shape of Pd nanocrystals is one of the main ways to enhance catalytic activity; however, the effect of shapes and electrolyte pH on carbon monoxide oxidation (COOxid) is not highlighted enough. This article presents the controlled fabrication of Pd nanocrystals in different morphologies, including Pd nanosponge via the ice-cooling reduction of the Pd precursor using NaBH4 solution and Pd nanocube via ascorbic acid reduction at 25 °C. Both Pd nanosponge and Pd nanocube are self-standing and have a high surface area, uniform distribution, and clean surface. The electrocatalytic CO oxidation activity and durability of the Pd nanocube were significantly superior to those of Pd nanosponge and commercial Pd/C in only acidic (H2SO4) medium and the best among the three media, due to the multiple adsorption active sites, uniform distribution, and high surface area of the nanocube structure. However, Pd nanosponge had enhanced COOxid activity and stability in both alkaline (KOH) and neutral (NaHCO3) electrolytes than Pd nanocube and Pd/C, attributable to its low Pd-Pd interatomic distance and cleaner surface. The self-standing Pd nanosponge and Pd nanocube were more active than Pd/C in all electrolytes. Mainly, the COOxid current density of Pd nanocube in H2SO4 (5.92 mA/cm2) was nearly 3.6 times that in KOH (1.63 mA/cm2) and 10.3 times that in NaHCO3 (0.578 mA/cm2), owing to the greater charge mobility and better electrolyte–electrode interaction, as evidenced by electrochemical impedance spectroscopy (EIS) analysis. Notably, this study confirmed that acidic electrolytes and Pd nanocube are highly preferred for promoting COOxid and may open new avenues for precluding CO poisoning in alcohol-based fuel cells.