While single-atom catalysts (SACs) have achieved great success in the past decade, their application is potentially limited by the simplistic single-atom active centers, which makes single-cluster catalysts (SCCs) a natural extension. SCCs with precise numbers of atoms and structural configurations possess SAC’s merits, yet have greater potentials for catalyzing complex reactions and/or bulky reactants. Through systematic quantum-chemical studies and computational screening, we report here the rational design of transition metal trimer clusters anchored on graphdiyne as a novel kind of stable SCCs with great potentials for efficient and precise heterogenous catalysis. By investigating their structures and catalytic performance for oxygen reduction reaction, hydrogen evolution reaction, and CO2 reduction reactions, we provide theoretical guidelines for their potential applications as heterogeneous catalysts. These graphdiyne supported SCCs provide an ideal benchmark scaffold for rational design of precise catalysts for industrially important chemical reactions.