The local treatment of periodontitis has recently received extensive attention due to the advantages of mild systemic side effects and a high local drug concentration. But the local drug delivery systems are not widely used in clinical practice, and a major obstacle is the poor tissue permeability. In the present study, we report a copper nanodot based ionic gel (Cu-NDs/IL gel) with favorable tissue penetration capability, and it concurrently exhibits antibacterial and anti-inflammatory functions. A Cu-NDs/IL gel was prepared by loading copper nanodots (Cu-NDs) with triple enzyme-like activities into a multifunctional gel. The derived Cu-NDs/IL gel possesses remarkable antibacterial properties attributed to the peroxidase-like activity of Cu-NDs. In addition, Cu-NDs mimic superoxide dismutase and catalase activities, which endow the gel with excellent free radical scavenging capability in a neutral environment to relieve periodontal inflammation. More importantly, the IL moiety in the Cu-NDs/IL gel promotes the penetration of Cu-NDs into the gingival tissue, wherein the triple enzymatic activity of Cu-NDs may function. In short, the Cu-NDs/IL gel has promising potential to serve as a topical drug for periodontitis by promoting penetration, killing bacteria, and scavenging ROS.