Metal sub-nanoclusters (SNCs) inherit the metrics of unsaturated active sites and ultrahigh metal utilization from single-atom catalysts (SACs), and they can drive the reactions involving multiple adsorbates by their enriched metal cofactors that beyond SACs. However, the current synthetic strategy offers limited versatility to prepare SNCs due to their subnanometric feature and high active surface. Herein, we demonstrate a universal and facile one-pot reaction to construct wide assortments of metal SNCs with the size of 2 to 3 nm on graphdiyne (GDY), denoted as M-SNCs/GDY (M = Co, Ni, Cu, Ag, Pd, Rh, Au, Ir, and Pt). Systematic investigations reveal that the correlated metal SNCs formation undergone the nucleation and growth process, during which the metal single-atoms were first anchored and then served as nuclei to grow SNCs confined on GDY. The electrochemical CO2 reduction reaction (eCO2RR) catalyzed by Cu-SNC/GDY and a Cu single-atom catalyst on GDY (Cu-SAC/GDY) was investigated to demonstrate the advantages of SNCs over SACs in manipulating the multicomponent reaction. Cu-SNC/GDY exhibited promoted Faradic efficiency (FE) of carbon products and suppressed competing hydrogen evolution reaction compared to the Cu-SAC/GDY. Benefiting from the function of multiple active centers, a C2+ FE of 31.6% was achieved over the Cu-SNC/GDY at −0.7 V versus reversible hydrogen electrode, which is 11-fold higher than that of Cu-SAC/GDY. In situ infrared spectroelectrochemistry confirmed that Cu-SNC/GDY could adsorb more eCO2RR intermediates over Cu-SAC/GDY. This study delivers a single-step strategy for preparing metal SNCs on GDY and expands the scope of SNCs.