Implantology has become a regular treatment in dentistry nowadays. However, dental implantology has just become popular, the complications have been more common. The main purpose of this article is to discuss the treatment outcome of bony defects in peri-implantitis with two kinds of bone substitutes. During the implant surgery, the exposed fixture surface was well treated with chemotherapeutic agent and laser decontaminated, two different kinds of bone powder substitues were used to fill the different sides of defect on the same dental implant for bone regeneration combined with resorbable membrane covered. After one year follow up, the X-ray film showed that the defect side with autogenous bone treated had better filling result than the side with freeze-dried bone substitute treated.