With the increasing demand for sustainable energy solutions, electrocatalysis has become an essential technology for energy conversion and storage. Despite significant advancements, traditional electrocatalysts still face persistent challenges in enhancing activity and improving stability. Recent studies have shown that vacancy engineering—modifying the atomic structure of materials through the introduction of vacancies—can significantly enhance catalytic efficiency and durability. As such, this approach provides a promising pathway to advance electrocatalysis. This review first explains the mechanisms of the hydrogen evolution reaction (HER) and oxygen evolution reaction (OER) and then provides a comprehensive overview of the application synthesis and characterization of various vacancies strategies, including anionic vacancies, cationic vacancy, and combined anionic–cationic vacancies. The review deeply analyzes the role of vacancies in the electrocatalysts for HER, OER, and overall water splitting. Moreover, the advanced characterization techniques for vacancies are introduced to demonstrate the effects of vacancies from the atomic level. Finally, the review addresses the current challenges and limitations associated with vacancy engineering and proposes potential directions for future research.