The pursuit of efficient hydrogenation nanocatalysts with a desirable selectivity toward intricate substrates is state-of-the-art research but remains a formidable challenge. Herein, we report a series of novel PdCdx nanocubes (NCs) for ultraselective hydrogenation reactions with flexible tuning features. Obtaining a desirable conversion level of the substrates (e.g., 4-nitrophenylacetylene (NPA), 4-nitrobenzaldehyde (NBAD), and 4-nitrostyrene (NS)) and competitive selectivity for all potential hydrogenation products have been achieved one by one under optimized hydrogenation conditions. The performance of these PdCdx NCs displays an evident dependence on both the composition and the use of Cd and a need for a distinct hydrogen source (H2 or HCOONH4). Additionally, for the selectivity of hydrogen to be suitably high, the morphology of the NCs has a very well-defined effect. Density functional theory calculations confirmed the variation of adsorption energy for the substrate and hydrogenation products by carefully controlled introduction of Cd, leading to a desirable level of selectivity for all potential hydrogenation products. The PdCdx NCs also exhibit excellent reusability with negligible activity/selectivity decay and structural/composition changes after consecutive reactions. The present study provides an advanced strategy for the rational design of superior hydrogenation nanocatalysts to achieve a practical application for desirable and selective hydrogenation reaction efficiency.