Here, we report a theoretical design of transition metals (TMs) anchored two-dimensional (2D) holey graphyne (HGY) based catalyst for the hydrogen evolution reaction (HER) through state-of-art density functional theory (DFT) simulation. The studied TMs (Co, Fe, Cr) are bonded strongly on HGY surface due to charge transfer from d orbital of metal to C 2p orbital of HGY. The HGY+TMs systems are stable at room temperature as evident from ab-initio molecular dynamics (AIMD) simulation. We predicted that the Co, Fe and Cr anchored HGY are highly active for HER activity with Gibbs free energy (ΔG) value as low as −0.21, −0.14, and −0.05 eV respectively and which are close to the best-known HER catalyst (Pt metal). The enhanced HER performance is attributed to the increased conductivity as well as redistribution of electrons. As pristine HGY is experimentally synthesized, HGY+TMs (Co, Fe, Cr) systems can be as an efficient catalyst for H₂ production.