Hydrogen evolution reaction (HER) is a promising route for sustainable hydrogen production. However, its efficiency is limited by kinetic barriers. Herein, we employ density functional theory (DFT) calculations to demonstrate a new strategy of embedding tetrametallic transition metal clusters (3TM1-TM2) into the pores of graphdiyne (GDY) to effectively optimize its HER performance. By screening 900 configurations, 10 prototypes displayed near-ideal hydrogen adsorption free energies. Among them, 3W–Hg@GDY with a ΔGH of −0.00035 eV was identified as the optimal candidate. Analysis of the electronic structure reveals hybridization between the metal d orbitals and GDY p orbitals near the Fermi level, creating partially filled impurity states to promote hydrogen adsorption. Additionally, coordination between the three TM1 atoms and active TM2 atom in the cluster enables precise tuning of TM2's electron density to achieve a moderate interaction with the adsorbed H, facilitating superior HER catalysis. Our findings showcase a new paradigm of cluster engineering for modulating GDY's reactivity that holds great promise as a universal approach for the design of high-performance GDY-based electrocatalysts beyond HER.