Abstract: Peri-implantitis, a common complication following dental implant surgery, arises from the dysregulated interplay between microbial infection and host immune responses, ultimately leading to peri-implant bone resorption and soft tissue inflammation. Conventional pharmacotherapy faces major challenges, including uncontrolled drug release, insufficient biofilm penetration, and poor local retention. Among these, achieving sustained antimicrobial efficacy at the lesion site remains a primary clinical hurdle. In recent years, hydrogel-based drug delivery systems have attracted considerable interest for peri-implantitis treatment owing to their tunable physicochemical properties, excellent biocompatibility, and ease of functional modification. This review outlines the design strategies and recent advances in functionalized hydrogel drug delivery systems for peri-implantitis, critically evaluates current research limitations, and offers a theoretical foundation for the development of novel localized drug delivery platforms.