Objective To compare the stress distributions in temporomandibular joint (TMJ) for patients with bilateral anterior disc displacement with reduction (ADDwR) after wearing stabilization splints with two different thicknesses during prolonged clenching by using three-dimensional (3D) finite element methods. Methods The 3D TMJ finite element models were constructed based on CT and MRI image data when the patient was biting in maximum intercuspation (working condition 1), on 3 mm thickness splint (working condition 2) and on 5 mm thickness splint (working condition 3), respectively. The von Mises stresses in the articular cartilages ,the TMJ disc and bilaminar zone under 3 working conditions were evaluated after the maximum jaw-closing forces were applied to the mandible for 60 s. Results The von Mises stress of left TMJ was bigger than that of right TMJ under each working condition. After wearing the 3 mm thickness splint, the disc was not recaptured, the stress was concentrated at the posterior band and bilaminar zone of the disc, and the stress on bilateral TMJ was significantly increased. After wearing the 5 mm thickness splint, the right disc was recaptured, the maximum stress was located at intermediate zone of the disc, and the von Mises stresses of articular cartilages and bilaminar zone were decreased by about 40%. However, the left disc was not recaptured, and the von Mises stresses of glenoid fossa cartilage and bilaminar zone were only slightly decreased by about 6%. Conclusions Different thicknesses of occlusal splints lead to different stresses and stress distribution patterns in TMJ of patients with ADDwR. The 5 mm thickness stabilization splint can reduce the stress of glenoid fossa cartilage and bilaminar zone in ADDwR patients. Disc recapture is helpful for ADDwR patients to relieve TMJ stress. When using stabilization splints for the treatment of ADDwR patients, on the premise of comfort wearing, a thicker splint can achieve more favorable stress distributions.