Modifying the spatial scale of active site has been proven a good strategy for enhancing catalytic performance. In this study, the Pd-based catalysts with different spatial scale of active site were constructed via the modification of non-metallic S or Si atoms over Pd, Cu alloyed Pd SACs, PdAg surface alloy and PdM (M=Au, Ag) IMCs catalysts, then, C2H2 semi-hydrogenation catalytic performance was identified based on DFT calculations. The findings indicate that the catalytic performance of C2H2 semi-hydrogenation is greatly influenced by the spatial extent of active site and the electronic effect modified by the S or Si atoms. Geometric effect caused by S or Si atoms reduces the spatial scale of active site over S/Pd-2 × 2, Si/Pd-3 × 3, S/Pd6Ag, S/Pd1Au1, S/Pd1Ag1 and Si/Pd1Ag1, thereby preventing green oil generation. Electronic effect caused by S or Si atoms leads to far away from the Fermi level of d-band center over S/Pd-2 × 2, Si/Pd-3 × 3, S/Pd1Au1, S/Pd1Ag1 and Si/Pd1Ag1 to improve C2H4 production activity and selectivity. Seven catalysts S/Pd-2 × 2, Si/Pd-3 × 3, PdCu-2 × 2, S/Pd6Ag, S/Pd1Au1, S/Pd1Ag1 and Si/Pd1Ag1 are screened out to present high selectivity and activity of C2H4 production, and effectively prevent green oil generation. This study provides valuable structural insights for designing high-performance catalysts by the modification of non-metallic atom in C2H2 semi-hydrogenation.