The invention discloses a method for encrypting a 3D model file and system thereof. The system of the invention comprises a data reading module used to read data of the 3D model file; a mesh shifting module for selecting at least one triangle mesh and shifting the coordinates of the vertexes of the selected triangle mesh by a vector; a gap filling module for filling a gap generated from shifting the vertexes of the selected triangle mesh by the vector to generate a revised 3D model file; and a model generating module for storing the revised 3D model file to generate an encrypted 3D model file. Compared to the prior art, the invention provides the users for previewing the 3D model file, and the invention only provides the authorized users for correctly printing the original 3D model. Therefore, the invention can achieve the purpose for encrypting the 3D model file.