Objective To explore the effects of antimicrobial peptides on the levels of periodontal inflammatory factors and bone metabolism factors in gingival crevicular fluid of patients with periodontitis. Methods A total of 108 patients with stage Ⅲ periodontitis in Department of Xinghai, Suzhou Stomatological Hospital were randomly divided into a control group, a minocycline group and an antimicrobial peptide group, with 36 patients in each group. The control group was given iodine glycerol in the periodontal pocket immediately and one week after scaling and root planing; the minocycline group was given minocycline hydrochloride, and the antimicrobial peptide group was given biological antimicrobial peptides. The differences in periodontal status (bleeding index (BI), probing depth (PD), attachment loss (AL)) between groups before and 30 d after treatment were compared through clinical examination. The inflammatory factors (matrix metalloproteinase-9 (MMP-9), interleukin-1β (IL-1β), tumor necrosis factor-α (TNF-α)) and bone metabolism indicators (alkaline phosphatase (ALP), bone γ-carboxyglutamic acid-containing protein (BGP), osteoprotegerin (OPG), SP7) in gingival crevicular fluid between three groups before and after treatment were compared through enzyme-linked immunosorbent assay (ELISA) detection. Results Before treatment, there were no statistically significant differences in periodontal indices (BI, PD, AL), inflammatory factors (MMP-9, IL-1β, TNF-α), and bone metabolism factors (ALP, SP7, BGP, OPG) among the three groups (P>0.05). Thirty days after treatment, all three groups showed significant improvement in various indicators compared to before treatment (P<0.05), and the indicators of the minocycline group and antimicrobial peptide group were better than those of the control group (P<0.05). In addition, the improvement of periodontal index BI, PD, and AL in the antimicrobial peptide group was better than that in the minocycline group (P<0.05); MMP-9, IL-1β were significantly lower in the antimicrobial group than in the minocycline group (P<0.05); ALP, SP7, BGP and OPG bone metabolism indicators were significantly higher than those in the minocycline group (P<0.05), but there was no significant difference in TNF-α levels between the two groups (P>0.05). Conclusion Biological antimicrobial peptides are significantly superior to minocycline hydrochloride in reducing periodontal inflammation and improving bone metabolism, and have potential for application as oral topical drugs for the treatment of periodontitis.