Periodontitis and orthodontic treatment present a complex interplay, where uncontrolled inflammation can exacerbate alveolar bone loss, while appropriately managed orthodontics can enhance periodontal stability. This conceptual paper proposes a novel mechanistic–clinical hybrid framework that integrates molecular biology, biomechanical principles, clinical risk stratification, and patient behavioral factors to guide orthodontic treatment in periodontitis patients. At the molecular level, cytokine profiles and inflammatory mediators drive alveolar bone remodeling, influencing responses to orthodontic forces. Biomechanically, force mechanics must be calibrated to minimize periodontal stress in compromised tissues. Clinical decision-making incorporates risk stratification based on disease staging and patient-specific factors, enabling real-time chairside adjustments. Patient behavior and adherence are embedded as modulators of treatment outcomes. This framework bridges the gap between pathophysiological insights and practical orthodontic planning, offering a multi-level synthesis that promotes periodontal stability during tooth movement. By linking molecular markers directly to force application and monitoring strategies, it facilitates personalized interventions, potentially reducing complications like further bone loss or tooth mobility. The model underscores the need for interdisciplinary collaboration between periodontists and orthodontists, advancing conceptual understanding in periodontology. Ultimately, this approach aims to optimize long-term periodontal health in orthodontically treated periodontitis patients.