In this case report, we investigated the effects of Ozone nanobubble water (ONBW) on peri-implantitis lesions with non-surgical treatment. ONBW preserves the ozone gas nucleus for more than 6 months although half life time of ozone water was almost 30 minutes. ONBW exerts anti-microbial activity towards several kinds of bacteria including periodontopathic bacteria and cariogenic bacteria. There was no cytotoxicity against oral epithelial and mucosa cells. The Advanced quick bonding (AQB) implants on 19 and 20 were placed on a patient 43 years old female four years ago. The chief complaint of her was swelling at the site of 20. The patient presented swollen at peri-implant area, Bleeding of probing (BOP), and probing depth (PD)=6 mm at buccal site of an implant of 20. There was no findings of mobility at concerned implant. The bone resorption and a radiolucent part around the implant was confirmed with periapical radiograph. The amount of bone loss was 5.0 and 6.5mm at mesial and distal site of 20, respectively. This peri-implantitis was evaluated the case required surgical therapy. In addition to mechanical plaque control, the patient received regular professional oral hygiene treatment and irrigation with ONBW every week at 100mL each. And also, regarding chemical plaque control, the irrigation for pockets was also performed at home by the patient at a frequency of three times a day every day. After 12 weeks, soft tissues of the peri-implant presented no clinical signs of inflammation and BOP, and PD was 3 mm. The bone levels did not change significantly as demonstrated by the follow-up roentgenography taken after 3 years. Microbiologically, the number of red-complex of periodontopathic bacteria have been decreased substantially. This case report supports that ONBW might be effective and predictable as an adjunctive therapy for peri-implantitis. To the best our knowledge, this is the first report on describing the peri-implantitis treatment with ONBW.