Objective This study aims to compare the clinical effects of therapy with vector ultrasonic system and periodontal flap surgery in patients with chronic periodontitis in a short time. Methods A total of 30 patients with chronic periodontitis were selected. The patients had deep pockets from 5 mm to 7 mm in both single-rooted teeth and multirooted teeth at 3 months after initial therapy. All patients were randomly divided into three groups. Each group had 10 patients. The patients were treated with vector ultrasonic system, periodontal flap surgery, and scaling and root planning, respectively. Patients were asked to report their perceived pain after 1 day of treatment by using a visual analog scale. The clinical parameters of bleeding on probing(BOP), probing depth(PD), gingival recession(GR), and clinical attachment loss(CAL) were recorded by Florida electronic probe at baseline, 3 months, 6 months, and 1 year. Differences were analyzed by SPSS 11.5. Results The three groups had differences in pain perception 1 day after the treatment. The vector ultrasonic system treatment group had the least pain reported, and the periodontal flap surgery group had the worst pain reported. For the study of the single-rooted teeth, the three groups had differences in PD, GR, and BOP after treatment in 3, 6, and 12 months compared with the baseline(PPPPP>0.05). Conclusion The vector ultrasonic system achieved better curative effect on single-rooted teeth than periodontal flap surgery 1 year after treatment. In multi-rooted teeth, the effect of the periodontal flap surgery was the most stable, whereas the other two treatments were unstable.