A three-dimensional conjugate tooth surface design method of Harmonic drive with a double-circular-arc tooth profile is proposed. The radial deformation function of the flexspline (FS) obtained by FEA is introduced into the kinematics model, and the optimization of the overlapping conjugate tooth profile is completed by analyzing the FS tooth enveloping process. Considering the hobbing process, the three-dimensional machinable tooth surface of FS is obtained. Considering the coning deformation of the FS, the multi-section assembly and meshing motion simulation of machinable tooth surface are carried out. Finite element method is used to analyze and compare the loaded contact characteristics. Results show that the proposed design method can obtain an internal gear pair composed of a circular spline with a spur gear tooth surface and a FS with a machinable tooth surface. Under the rated torque, 24% of the FS teeth are engaged in meshing, and more than 4/5 of the tooth surface in the axial direction carries the load. The contact patterns, maximum contact pressure and transmission error of the machinable tooth surface are 227.2%, 40.67%, and 71.24% of the spur gear tooth surface respectively, showing excellent transmission performance.