Searching for catalysts of hydrogen evolution reaction (HER) that can replace Pt is critical. Here, we investigated the HER electrocatalytic activity of pentagonal PdS₂ (penta-PdS₂) and PdSe₂ (penta-PdSe₂) by first-principles calculations. Three types of vacancies (V_S/Se, V_Pd, DV_S/Se) were constructed to activate the inert basal planes of PdS₂ and PdSe₂. The results show that S/Se and Pd vacancies significantly improve HER performance, and the Gibbs free energy (ΔG_H) of systems can be further regulated by vacancy concentration. Particularly, PdS₂ with 2.78% V_S, 50% V_Pd and PdSe₂ with 12.5% V_Se display the optimal ΔG_H value and the highest exchange current density. Further analysis of charge transfer and band structures were described that the introduce of vacancies efficiently regulates the electronic properties, resulting in the diminution of bandgap, and accelerates the charge transfer, thereby contributing to an enhanced electron environment for HER process. Our results provide a theoretical guidance for the applications of pentagonal transition-metal dichalcogenides as catalysts of hydrogen evolution reaction.