Gears are usually measured by the contact metrology method in gear measuring centers or coordinate measuring machines. Recently, three-dimensional (3D) optical scanning, a non-contact metrology method, has been applied in the industry as an advanced measurement technology mainly due to its high efficiency. However, its applications to gears with complicated geometry, such as face gears, are still limited due to its relatively low accuracy and the void of related measurement solutions. In this work, an accurate measurement solution with 3D optical scanning is proposed for the tooth surface deviations of orthogonal face gears. First, point cloud collection is carried out by the 3D scanner. Furthermore, the measurement solution is implemented with a three-stage algorithm by aligning point clouds with the design model. Subsequently, 3D modeling is studied by numbering the points and reconstructing the real tooth surfaces. An example with a measurement experiment and loaded tooth contact analysis is given to show the validity of the proposed method.