Objective To reconstruct three-dimensional finite element model with occlusion and bilateral condyles to analyze the regularities of TMJ stress distribution resulting from dental occlusion alteration. Methods A skull was scanned with CT in the direction parallel to the Frankfort Horizontal plane. Occlusion surface of it's plaster casts were scanned with a 3D scanner. The parameters of the cast and CT image were converted into the same coordinate system. A simulated disc was added over each of the condyles. Constraints were applied to the upper surface of the disc and the angle of mandible. Load 1: Onto the different positions of the teeth in half of the dentition, FEM were applied with upright loads. Load 2: Onto three different occlusal areas of the lower second molar, ICO load.distal load.buccal load were applied. The stresses on condyle under each of the conditions above was analyzed. Results 1. The FEM containing bilateral condyles.simulated discs, and dental occlusion was formed to analyze the association of occlusion and TMJ.2. As occlusal load was applied to different teeth on dentition from anterior to posterior, the stress distribution of bilateral condyles were found different and asymmetrical. The lateral, middle, anterior and top area of condyle were found loading with high compression. 3. The morphological features of loading area had effect on the stress characteristics and distribution of bilateral condyles. Loading from distal direction would cause stress concentrating over the medial pole of ipsi-lateral condyle while loading from buccal direction would cause stress concentrating over the medial pole of contra-lateral condyle. Conclusion The distribution of stress over condyles was found changed in response to the alternation of occlusal contact position and direction.