The invention relates to a bidirectional conjugate tooth profile design method for harmonic gear drive. The bidirectional conjugate tooth profile design method for harmonic gear drive comprises the steps of firstly, expressing a flexible wheel top-section convex tooth profile coordinate through a parameter equation, converting to a rigid wheel coordinate system, solving to obtain discrete point coordinates of a theorical conjugate concave tooth profile and a concave tooth profile of a flexible wheel top-section convex tooth profile, determining the working tooth depth of a rigid wheel tooth profile through least square fit, determining a fitted curve section to be a rigid wheel bottom-section concave tooth profile and a rigid wheel top-section concave tooth profile, and calculating to accomplish a tooth profile design of a rigid wheel; and then expressing a rigid wheel top-section convex tooth profile coordinate through a parameter equation, converting to a flexible wheel coordinate system, solving to obtain discrete point coordinates of a theorical concave conjugate tooth profile in a flexible wheel bottom-section range, determining the tooth depth of a flexible wheel through least square fit, determining a fitted curve to be a flexible wheel bottom-section concave tooth profile, and calculating to obtain a flexible wheel working tooth profile. According to the bidirectional conjugate tooth profile design method for harmonic gear drive provided by the invention, the flexible wheel tooth profile and the rigid wheel tooth profile with bi-conjugate and secondary-conjugate phenomena are directly obtained, so that a conjugate contact area and a meshing zone are increased, the tooth surface contact stress is reduced, and the drive accuracy of a harmonic reducer is improved.