Objective To explore the effects of facial asymmetry on stress distributions in temporomandibular joints (TMJs) for patients with mandibular prognathism. Methods Eight 3D maxillofacial models were established in MIMICS based on cone-beam CT of 4 mandibular prognathism patients with asymmetry and 4 mandibular prognathism patients without asymmetry. Muscle forces and boundary conditions corresponding to the unilateral occlusion (unilateral molar chewing) were applied on the models in ABAQUS. The maximum and the minimum principal stresses of TMJ were chosen for analysis. Results There were significant differences in the maximum and minimum principal stresses at the condyles between the mandibular prognathism patients with and without facial asymmetry under unilateral occlusions (P<0-05). Compared with patients without facial asymmetry, the stresses on the condyle in patients with asymmetry increased by 2-3 times, and the stresses on articular fossa increased by 5-7 times. Among the mandibular prognathism patients with asymmetry, the stresses of the ipsilateral TMJ in patients with temporomandibular disorder (TMD) were significantly higher than those in patients without TMD. Conclusions Facial asymmetry increased the stresses of the articular fossa and condyle in patients with mandibular prognathism. TMD would cause greater stresses in ipsilateral TMJ of the mandibular prognathism patient with asymmetry. Therefore, different treatment strategies should be considered for mandibular prognathism with facial asymmetry.