Heterogeneous solid catalysts based on atomically dispersed Pd species are the most applicable catalysts in selective alkyne hydrogenation. However, the understanding of their structure–activity relationship remains ambiguous due to lack of structural analysis tools available and a unified synthetic system to obtain comparable Pd-based catalysts. Herein, we reported a convenient method to obtain Pd nanoclusters and Pd single atoms loaded on a nitrogen-doped carbon support (marked as Pd-NC@NC and Pd-SA@NC, respectively) in a uniform procedure and explored their structure–activity relationship in phenylacetylene hydrogenation. By the application of various kinds of characterization methods, we legibly illustrated the structures of Pd-NC@NC and Pd-SA@NC and found that Pd-NC@NC exhibited much higher mass activity than Pd-SA@NC (6.70 vs 0.33 mmol g–1 h–1) in phenylacetylene semi-hydrogenation. Theoretical calculations revealed that the different abilities of Pd nanoclusters and Pd1-N4 sites to adsorb reactants caused by steric hindrance were most likely to contribute to their different catalytic performances. This established structure–activity relationship provides guidelines for rationally designing metal catalysts for selective alkyne hydrogenation.