Objective: To compare the clinical effects of periodontal treatment using periodontal endoscope with that of conventional treatment method for patients with periodontitis. Methods: Eleven periodontal patients with moderate to advanced periodontal destruction were recruited and treated with scaling and root planing in a split-mouth design randomly with (test group) or without (control group) periodontal endoscope. Changes of such clinical parameters as plaque index (PLI), bleeding index (BI), probing depth (PD) and attachment loss (AL) before and after treatments as well as the difference between test and control groups were examined and compared. Results: Both groups showed significant reductions in PD, BI and AL values at 6 weeks and 3 months after treatment (P <0.001). Only in the test group, for sites with PD≥6 mm at baseline, PD value ([4.0±1.2] mm) and AL value ([3.8±0.9] mm) at the end of 3 months were significantly lower than that at the end of 6 weeks (PD[4.4±1.3] mm, P<0.001; AL[4.1±1.1] mm, P< 0.05). There were no significant differences between two groups at the baseline, at the end of 6 weeks and 3 months, respectively. However, for the sites with PD≥6 mm in anterior teeth, PD value in test group at the end of 3 months was significantly lower than that in control group ([3.2±0.9] mm vs [3.7±0.9] mm, P <0.05), while AL value tend to be lower ([2.9 ± 1.2] mm vs [3.6 ± 1.3] mm, P=0.061). Conclusions: Periodontal treatment using endoscope is obviously effective, especially for the medium and long term prognosis of deep pockets and single rooted teeth.