Palatogingival groove (PGG), a congenital developmental defect, accelerates localized periodontal destruction by creating anatomic plaque-retentive niches and complex periodontal pockets. This case report describes a 30-year-old male with generalized stage Ⅲ grade C periodontitis, combined with PGG on tooth #12 and Angle Class Ⅰ malocclusion. Multidisciplinary management involved four phases: (1) Initial periodontal therapy (scaling and root planing with oral hygiene reinforcement) to suppress active inflammation; (2) Surgical intervention (open flap debridement from #13 to #21 with concomitant flowable resin sealing of the PGG on #12) to eliminate microbial reservoirs; (3) Orthodontic treatment (diastema closure and functional occlusal reconstruction) to remove traumatic occlusal forces; (4) Long-term supportive periodontal care (6-month recall visits). At 2-year follow-up, the percentage of sites with probing depth (PD) ≥4 mm decreased from 48% (baseline) to 27%. Tooth #12 exhibited localized angular bone loss palatally but increased radiodensity apically, with significant functional and aesthetic improvements. The key findings of this article were as follows. (1) Flap surgery combined with PGG sealing effectively eradicated infection and blocked anatomic pathways. (2) Periodontal-orthodontic synergy simultaneously controlled inflammation and corrected occlusal trauma. (3) Staged multidisciplinary sequencing provided a replicable framework for managing complex periodontitis.