Objective: To investigate the efficacy of antibacterial peptides in the adjuvant therapy of stage Ⅲ periodontitis. Methods: Fifty-one patients were randomly divided into simple mechanical curettage group, minocycline hydrochloride group and antibacterial peptide group according to the treatment mode. Three groups received periodontal sequential treatment, and after the ultrasonic supragingival scaling, they were performed with curettage, root surface planing, polishing and flushing. After treatment in the minocycline hydrochloride group and the biological antibacterial peptide group, minocycline hydrochloride ointment and biological antibacterial peptide periodontal gel were injected into the periodontal pocket respectively. The mechanical curettage group did not take medicine. Periodontal checklists at baseline and 90 d after treatment were recorded to compare differences of the three groups in periodontal probing depth (PD), bleeding index (BI) and attachment level (AL). Enzyme-linked immunosorbent assay (ELSIA) was used to detect the change of tumour necrosis factor-α (TNF-α), interleukin (IL)-1β by collecting the gingival crevicular fluid of the three sets at baseline, 7 d after treatment and 90 d after treatment. Results: There was no statistically significant difference in periodontal clinical examination indexes(PD,BI,AL) and contents of TNF-α and IL-1β in the gingival crevicular fluid between the three groups at baseline (P>0.05). At 7 and 90 d after treatment, all indexes in the three groups were improved compared with those before treatment. The comparison between groups showed that in periodontal pockets with PD≤5 mm, there was no statistically significant difference in the indicators between the three groups. In periodontal pockets with PD≥6 mm, the minocycline hydrochloride group and the bio-antibacterial peptide group had no statistically significant difference in various indicators, but they were all better than the mechanical scaling group. Conclusion Basic periodontal therapy is an important treatment for stage Ⅲ periodontitis. Minocycline hydrochloride and biological antibacterial peptides are both effective adjuvant drugs for deep periodontal pockets with PD≥6 mm.