Meshing backlash mainly determines the transmission accuracy of harmonic drive, which is an important index in design. In this paper, a design method of short tooth involute profile is proposed, which relies on positive modification to enhance the strength of dedendum. By intercepting part of tooth profile, the meshing interference of addendum can be effectively avoided. Based on the dimensions of over pins of circular spline and flexspline, a calculation method of tooth thickness deviation is proposed, and the positive and negative of tooth thickness deviation are defined. Involute functions need not be calculated by this method, which simplifies the solution process. By discretizing the teeth profile points of circular spline and flexspline, a calculation method of time-varying backlash is proposed, the variation of backlash in the process of meshing in and out is analyzed, and the influence law of tooth thickness deviation on backlash is studied. On this basis, an algorithm of adjusting the radial deformation to compensate the backlash is proposed. The results show that the excessive backlash in the meshing area can be reduced by increasing the radial deformation. when meshing interference occurs, the interference free meshing can be realized by decreasing the radial deformation.