Mandibular prognathism, retrusion and deviation are common mandibular deformities. They can lead to functional and aesthetic problems due to their important role in the oral system. Different from other occlusions, unilateral molar occlusion often occurs during mastication, which has a deep impact on the functions of temporomandibular joints (TMJs). Therefore, the study of unilateral molar occlusion is of great importance and significance to the daily life of patients with mandibular deformities. A total of 35 individuals were involved in this study, including 11 asymptomatic subjects, 10 patients with mandibular prognathism, 5 patients with mandibular retrusion and 9 patients with mandibular deviation. Finite element (FE) models corresponding to the unilateral molar occlusion were constructed. During unilateral molar occlusion, mandibular deformity increases the pressure on the condyle and articular disc. Compared with mandibular protrusion or retraction, facial asymmetry will significantly increase the stress of TMJ. Chewing on the non-deviated side also will lead to higher stress in the TMJ of patients with mandibular deviation. Therefore, patients with mandibular deviation have the highest risk of temporomandibular disorder (TMD), and it is recommended that patients with mandibular deviation chew bilaterally or with the deviated side.