Semi-hydrogenation of acetylene is of growing interest and popularity but subjects to a major challenge in selective hydrogenation to ethylene. Here, we report a strategy that uses graphdiyne (GDY) as a carrier to prepare single-cluster catalysts (SCCs), which on average clusters composed of three atoms (denoted as Pd₃ trimer) and applied it to the acetylene semi-hydrogenation in the presence of large amounts of ethylene. Based on experimental results and systematic quantum chemical research and computational screening, we found that there are multiple active Pd structures on GDY and the Pd₃ trimer anchored on GDY is a specific and durable cluster with great potential for accurate and efficient heterogeneous catalysis. The synergetic effects between neighboring atoms in Pd trimer guarantee easy desorption of ethylene and the absence of unselective hydride species thereby preventing excessive hydrogenation to generate unwanted byproducts, which is a crucial mechanism for the excellent selectivity of the catalyst. This new method for precise synthesis Pd clusters provides accurate ways for designing selective hydrogenation catalysts at the atomic scale.