Abstract: Objective: To compare change in PD(periodontal probing), CAL(clinical attachment loss) and ABD(alveolar bone density) between the initial therapy and initial therapy flap surgery groups from baseline to end of follow-up(6 months). Methods: Patients with severe chronic periodontitis were observed in the initial therapy group(20) and the initial therapy flap surgery group(20). Totally 40 patients were followed up for 6 months after both treatment.Outcomes for PD, CAL and ABD for each tooth were collected at two time points(baseline and 6 months after treatment). Descriptive analysis was used to summarize the demographic characteristics. A mixed-model ANCOVA will be conducted, controlling for covariates of baseline outcome value, age, sex and alcohol intake, to evaluate the treatment difference between the initial therapy group and initial therapy flap surgery group in change from baseline of the outcomes. Results: A total of 145 teeth(72 in the initial therapy group, and 73 in the initial therapy flap & surgery group) were evaluated. Teeth that received the initial therapy flap surgery group performed better in change from baseline of PD than teeth that received the initial therapy group(-1.25 vs.-2.00, P<0.001). There is no statistical significance treatment difference in change from baseline of CAL between two groups. Teeth that received the initial therapy flap surgery group performed better in change from baseline of BMD than teeth that received the initial therapy group(0.027 vs. 0.059, P<0.001). Conclusion: There may be substantial benefits for patients who received the initial therapy flap surgery group than the initial therapy group only. CBCT could be used in evaluation of alveolar bone changes in the Sequence of periodontal treatment of chronic periodontitis