Harmonic drives (HDs) with short flexspline (FS) always suffer from small meshing areas and severe stress concentration caused by large cone angles when a short FS is assembled and loaded. To address this issue, a tooth longitudinal modification method for the circular spline (CS) with a double circular arc common-tangent tooth profile (DCTP) is proposed. Using neutral layer and envelope conjugation theories, a mathematical model of the conventional straight CS tooth was developed. A shaping cutter for this tooth profile was then designed through coordinate transformation and meshing principles. The proposed longitudinal modification for the CS was achieved by adjusting the cutter’s trajectory. A precise finite element model of the HD was developed, revealing that tooth longitudinal modification can reduce the maximum contact pressure by 69.6% and significantly increase the contact area for HDs with short FS. This work provides valuable technical references for improving the contact state of HDs with short FS.