In order to improve the measurement accuracy of non-circular gears, a three-dimensional measurement method for non-circular gear tooth surfaces is proposed. According to the basic meshing principle of the non-circular gear, the tooth surface model of the non-circular gear is established, and the three-dimensional solid modeling of the non-circular gear is completed. In order to reflect the geometry information of the tooth surface more realistically, a method of sampling the tooth surface with equal arc length by using the intersection line is proposed, and the non-circular gear tooth surface is meshed. Taking the elliptical gear as an example, the three-dimensional solid model of the non-circular gear is obtained by Einscan-SP scanner. The Geomagic Qualify software is used to align the solid model with the theoretical model, and the aligned tooth flanks are meshed to obtain the three-dimensional error value of the tooth surface of non-circular gear. This method eliminates the influence of the two-dimensional positioning error on the measurement accuracy and improves the measurement accuracy of the non-circular gear.