Objective: This study was designed to determine the efficacy of minocycline hydrochloride ointment (MHO) combined with Vitapex paste on middle-aged and elderly patients with combined periodontal-endodontic lesions (CPELs) and its effect on the inflammatory factors. Methods: The data of 88 elderly patients with CPELs treated in the First Affiliated Hospital of Gannan Medical University from March 2020 to March 2022 were analyzed retrospectively. Among them, the patients treated with MHO and iodoform zinc oxide clove oil paste were assigned into the control group (n = 42) and the rest of the patients treated by MHO and Vitapex paste were assigned to the study group (n = 46). The inflammatory factors, periodontal indexes and efficacy were determined and compared between the two groups. The MOS 36-Item Short-Form Health Survey (SF-36) was adopted to evaluate the quality of life (QoL) of patients before and after treatment. Additionally, the adverse reactions of the two groups during treatment were analyzed and compared. The prognosis of the two groups of patients was analysed, and factors impacting their prognosis was analysed through the Logistic regression analysis. Results: Before treatment, the levels of interleukin-6 (IL-6), tumor necrosis factor-α (TNF-α) and interleukin-1β (IL-1β) were not significantly different between the two groups (all P > 0.05), while after treatment, these levels in both groups decreased significantly, with notably lower levels in the study group than those in the control group (all P < 0.05). Before treatment, the gingival index (GI), plaque index (PLI), probing depth (PD) and bleeding index (BD) of the two groups were similar (all P > 0.05); however, after treatment, the levels of GI, PD, PLI and BI of both groups decreased significantly (all P < 0.05), with more notable decreases in the study group than those in the control group (all P < 0.05). The study group showed a significantly higher overall response rate than the control group (P < 0.05). Before treatment, the SF-36 scores of the two groups were not significantly different (P > 0.05), while after treatment, both groups had significantly increased SF-36 scores, and the score in study group was significantly higher than the control group (P < 0.05). In addition, the incidence of adverse reactions was not notably different between the two groups (P > 0.05). According to univariate analysis, age, dental lesion grade, course of disease, and persistent dull pain were the risk factors affecting the prognosis of patients. According to multivariate analysis, dental lesion grade was the independent risk factor affecting the prognosis. Conclusion: MHO combined with Vitapex paste is effective for middle-aged and elderly patients with CPELs, which can effectively inhibit the patients' inflammatory reaction and improve their periodontal condition and QoL, with a low adverse reaction rate, so it is worthy of clinical promotion.