Peri-implantitis, caused by bacterial biofilm on dental implants, leads to bone loss and tissue inflammation, ultimately causing oral health decline. Traditional methods to remove biofilm are ineffective in promoting reosseointegration on implant surfaces. This phenomenon can be attributed to two factors: incomplete removal of biofilm from hard-to-reach areas and alterations in the physicochemical properties of implant surfaces caused by decontamination procedures. To address this problem, we developed D-arginine-loaded chitooligosaccharide-capped pH-responsive mesoporous silica nanoparticles (Dar@MSN-COS) for improving the efficacy of decontamination of Water Jet (WJ). Dar@MSN-COS particles exhibit a targeted approach towards the extracellular polymeric substance (EPS) in order to disrupt the biofilm, and possess the capability to infiltrate confined areas between implant screws. Following this, the WJ treatment effectively removed residual biofilm and demonstrated improved cleaning efficacy. Furthermore, the decontamination of the Dar@MSN-COS combination with WJ promotes effective cell cytocompatibility on the titanium surface. The results of mechanistic experiments indicate that Dar@MSN-COS may act on biofilms by releasing a significant quantity of reactive oxygen species (ROS), suggesting it as a key contributing factor. In summary, our novel therapeutic protocol shows promise as an alternative solution for addressing the clinically complex aspects of peri-implantitis.