Objective To investigate the efficacy of minocycline hydrochloride combined with microscopic root canal and periodontal tissue regeneration in the treatment of endodontic-periodontal lesions with root groove deformity.Methods A total of 102 patients (102 teeth in total) with endodontic-periodontal lesions combined with root groove deformity in our hospital from April 2020 to January 2022 were selected and divided into the control group and the study group by the random number table method, with 51 cases in each group. The control group was treated with microscopic root canal and periodontal tissue regeneration, and the study group was additionally treated with minocycline hydrochloride. The success rate of surgery, periodontal indices, levels of inflammatory factors, masticatory function scores, pain and complications were compared between the two groups.Results The 1-year success rate of surgery in the study group (90.20%) was higher than that in the control group (72.55%) (P < 0.05). The differences of sulcus bleeding index, probing depth, calculus index, plaque index, levels of C-reactive protein, tumor necrosis factor-α, and interleukin-17, masticatory function scores, and Visual Analogue Scale scores before and after the treatment in the study group were greater than those in the control group (P < 0.05). There was no difference in the overall incidence of complications between the two groups (P > 0.05).Conclusions Minocycline hydrochloride combined with microscopic root canal and periodontal tissue regeneration is effective in the treatment of patients with endodontic-periodontal lesions with root groove deformity. It improves the periodontal health and ameliorates inflammation and pain.