Abstract Peri‐implantitis is an inflammatory disease characterized by progressive bone loss, challenging implant longevity and incurring significant treatment burden. Current reconstruction therapy involves mechanical scaling followed by artificial bone grafting. However, residual bacteria and inflammation memory often lead to recurrence, highlighting the critical need for the artificial bone substitute with sustained anti‐inflammatory and antibacterial properties. By utilizing the phosphate groups of mesoporous hydroxyapatites for in situ loading of CeO 2 , followed by a reduction method to fabricate a CeO 2 ‐Cu heterojunction interface, this study develops Bonyzymes with anti‐inflammatory, antibacterial, and osteogenic properties. The incorporation of Cu modulates the electronic environment of the CeO 2 surface, increasing superoxide dismutase and catalase activities of Bonyzymes. In vitro, the Bonyzymes effectively regulated oxidative stress by scavenging excess reactive oxygen species, exerting anti‐inflammatory effects. Additionally, it exhibits antibacterial activity against Staphylococcus aureus , Escherichia coli and Porphyromonas gingivalis , and facilitates osteogenic differentiation in bone marrow stem cells. In vivo experiments in rat peri‐implantitis models confirm its ability to promote bone regeneration in the infected peri‐implant area. Overall, this work develops novel artificial bone substitutes, Bonyzymes, which not only promotes bone regeneration but also exhibits anti‐inflammatory and antibacterial properties, offering a promising strategy for peri‐implantitis treatment.