Heterostructured nanomaterials have arisen as electrocatalysts with great potential for hydrogen evolution reaction (HER), considering their superiority in integrating different active components but are plagued by their insufficient active site density in a wide pH range. In this report, double sulfur-vacancy-decorated CoS1.097@MoS2 core-shell heterojunctions are designed, which contain a primary structure of hollow CoS1.097 nanocubes and a secondary structure of ultrathin MoS2 nanosheets. Taking advantage of the core-shell type heterointerfaces and double sulfur-vacancy, the CoS1.097@MoS2 catalyst exhibits pH-universal HER performance, achieving the overpotentials at 10 mA cm-2 of 190, 139, and 220 mV in 0.5 M H2SO4, 1.0 M KOH, and 1.0 M PBS, respectively. Systematic theoretical results show that the double sulfur-vacancy can endow the CoS1.097@MoS2 core-shell heterojunctions with promoted electron/mass transfer and enhanced reactive kinetics, thus boosting HER performance. This work clearly demonstrates an indispensable role of double sulfur-vacancy in enhancing the electrocatalytic HER performance of core-shell type heterojunctions under a wide pH operating condition.