Objective: To investigate the effects of different root canal filling techniques combined with iRoot SP on the periodontal aesthetic score and inflammatory marker levels in gingival crevicular fluid (GCF) of patients with endodontic-periodontal diseases, and to provide clinical evidence for optimizing root canal filling strategies.Methods: A total of 60 patients with endodontic-periodontal diseases treated in the Department of Stomatology of a certain hospital from March 2023 to February 2025 were randomly assigned to a control group and an experimental group (30 cases each) using a random number table method. The control group received traditional lateral compaction root canal filling combined with iRoot SP, while the experimental group received warm gutta-percha vertical compaction root canal filling combined with iRoot SP. Periodontal aesthetic scores were assessed before treatment and three months after treatment. Levels of hypersensitive C-reactive protein (hs-CRP), tumor necrosis factor-alpha (TNF-α), and interleukin-1β (IL-1β) in GCF were measured. Clinical efficacy was also recorded.Results: After treatment, the periodontal aesthetic score in the experimental group was significantly better than that in the control group (P < 0.05). Levels of hs-CRP, TNF-α, and IL-1β in the GCF were significantly lower in the experimental group than in the control group (P < 0.05). The total effective rate was higher in the experimental group (P < 0.05), and the incidence of complications was lower (P < 0.05).Conclusion: Compared with the traditional filling method, the warm gutta-percha vertical compaction technique combined with iRoot SP can significantly improve the periodontal aesthetic outcome, reduce levels of inflammatory factors, enhance treatment efficacy, and has greater clinical application value.