Objective To analyze effects of different elastic modulus, thickness and tooth movement on deformation of the invisible dental appliance by finite element method, so as to provide theoretical references for orthodontic doctor to formulate the orthodontic treatment scheme. Methods A total of 12 finite element models of invisible appliances were established with 4 kinds of thickness and 3 kinds of elastic modulus. The displacement load of the tilting movement was applied to the 12 models, and the maximum Von Mises stress and deformation of the appliance were analyzed; the deformation of the appliance was analyzed by applying the displacement load of inclined, parallel and intrusion to the optimal model. Results The maximum Von Mises stress increased with the elastic modulus and thickness of the invisible appliance increasing. The deformation decreased with the appliance thickness increasing. When the tooth was under inclined and parallel movement, the maximum deformation was found in the corresponding part of the tooth. Some of the corresponding parts of the immovable teeth were deformed to the lip convex side and some to the tongue side with internal concave deformation, and the appliance deviated seriously to top of the crown when the tooth was under intrusion movement. Conclusions The optimum thickness of invisible dental appliance was 0.75 mm, and the elastic modulus 816.31 MPa that currently used in clinic was suitable. In the digital model, the tongue side of the teeth corresponding to the labial protruding part and the lip side of the tooth corresponding to the concave side of the tongue side can be thickened, and the invisible appliance can be optimized by using the thickened digital model.