Background: The objective of this study was to evaluate and compare the expression levels of TNF-alpha, omentin-1, and IL-6 in periodontitis patients before and after treatment with biological antimicrobial peptide (AMP) periodontal gel. Methods: There involved 86 periodontitis patients admitted to our hospital from January 2020 to March 2021. They were equally and randomly distributed into the study group and the control group. The efficacy and adverse reactions were compared between the two groups after treatment, Additionally, the sulcus bleeding index (SBI), plaque index (PLI), gingival index (GI), periodontal probing depth (PD), and levels of TNF-alpha, omentin-1, and IL-6 were measured before and after treatment. Results: After treatment, the total effective rate of the study group was significantly higher than that of the control group (p < 0.05), while the scores of four indicators (SBI, PLI, GI, and PD) and the levels of TNF-alpha, omentin-1, and IL-6 in the study group were evidently lower than the control group (p < 0.05). The study group had 1 case of mild irritant reaction, with an adverse reaction rate of 2.33% (1/43). And the control group had 1 case of nausea and 1 case of allergy, with an adverse reaction rate of 4.65% (2/43). The adverse reactions demonstrated no statistical difference between the two groups (chi(2) = 0.345, p = 0.557). Conclusions: The levels of TNF-alpha and IL-6 were highly expressed before the auxiliary therapy of biological AMP periodontal gel for periodontitis, alongside low expression of omentin-1. Subsequently, the biological antibacterial polypeptide periodontal gel demonstrated efficacy in the treatment of periodontitis.