Green hydrogen production from electrocatalytic water splitting is drawing growing interests to meet the needs of sustainable development. The efficiency of water splitting is governed by the electrocatalysts for hydrogen evolution reaction (HER) and oxygen evolution reaction (OER). Atomic vacancies have demonstrated significant advancements to modulate the electrocatalytic performance. Herein, the latest progresses of atomic vacancy engineering are systematically summarized, including the representative methods for generating different vacancies, the advanced microscopic and spectroscopic techniques for identifying vacancies, and the electrochemical and theoretical approaches for understanding the effect of vacancies and exploiting new atomic vacancies. The internal relations between specific vacancy regulation route and enhanced catalytic performance are discussed in terms of the improved electronic structure, the lowered energy barrier, and the optimized adsorption/desorption behavior of intermediate species. Beyond that, the synergistic effects between atomic vacancy and dopant/ single-atom/ nanocluster/ heterojunction are elucidated. At the end, instructive outlooks are proposed for in-depth understanding on atomic vacancies and scaling-up water splitting for the industrial application.