Objective To explore the effect of periodontal sequence therapy combined with gingival contouring on periodontal health indicators in patients with periodontal disease complicated by gingival papilla deffciency. Methods A total of 60 patients with periodontal disease complicated by gingival papilla deffciency admitted to Yancheng Stomatological Hospital from August 2023 to August 2025 were selected as the research subjects. According to the random number table method, they were divided into the control group and the observation group, with 30 patients in each group. The control group was treated with periodontal sequence therapy, and the observation group was treated with gingival contouring on the basis of the control group. The periodontal health indicators, aesthetic effect and adverse reaction rate were compared between the two groups. Results At 3 months after treatment, the levels of PLI, BI, PD and GI in the observation group were lower than those in the control group (P<0.05). At 1 and 3 months after treatment, the scores of PES in the observation group were higher than those in the control group (P<0.05). The incidence of adverse reactions in the observation group (66.67%) was higher than that in the control group (23.33%) (P<0.05). Conclusion Periodontal sequence therapy combined with gingival aesthetic contouring can improve periodontal health and aesthetic effect, but has a higher risk of adverse reactions. Clinical application needs to balance efffcacy and postoperative management, and strengthen risk prevention and control while pursuing dual beneffts of function and aesthetics.