The symmetrically stable craniofacial bony structure supports the complex functions and delicate contour of the face. Congenital craniofacial deformities are often accompanied by bony defects and have been repetitively correlated with compromised dento-maxillary stability, but neither the extent nor the pattern of cleft-related maxillary instability has been explored in detail. Furthermore, it is largely unknown if the bony defect and related instability are correlated with secondary maxillary deformity common among patients with orofacial clefts. With the aid of finite element modeling, we studied the detailed relationship between cleft-related bony defect and maxillary stability under occlusal loading. Craniofacial models were generated based on cone-beam computed tomography data and loaded with mimicked bite forces along the axial axis of each tooth. Our data showed that all cleft models exhibited more asymmetrical deformations under mastication compared with the normal. Models with palatal cleft demonstrated greater asymmetry, greater dental arch contraction, and less maxillary protrusion compared to models with alveolar cleft only. For unilateral cleft models, alveolus on non-cleft side tended to be more protruded and lifted than the cleft side. For bilateral cleft models, the most prominent feature was the seriously contracted alveolar arch and curved and pitched premaxillae. These findings indicated cleft type-specific pattern of maxillary instability, which were largely in accordance with dentoalveolar morphological features among patients. Collectively, our study elucidated the detailed relationship between cleft bony defect and the pattern of maxillary instability, and suggested a prototype for studying the abnormal maxillary and dental arch growth among patients with craniofacial deformities.