The experiment was designed based on the response surface theory to study the influence about various manufacturing errors of harmonic gears on the tooth surface stress and wear of the flexspline. A four-factor response surface model was adopted, which includes the span value (M-value) deviation of the flexspine, the M-value deviation of the circular spline, the long half axis deviation, and the short half axis deviation of the wave generator. Then corresponding harmonic gear models were established for finite element simulation analysis, respectively. The experimental results show that the cam long half axis deviation is most sensitive to the stress on the flexspline tooth, the M-value deviation of the flexspline and the M-value deviation of the circular spline less, and the cam short axis deviation sensitivity the least. Four kinds of error compensation schemes were proposed for different deviations of the gears of the circular spline and the flexspline, which may occur during the manufacturing process, to improve the meshing condition and the accuracy retention. That is, the long half axis of the cam can be reduced when the M-values of the flexspline and the circular spline are both negative deviation, or positive and negative deviation respectively; the long half axis of the cam can be increased when the M-values of the flexspline and the circular spline are both positive deviation, or negative and positive deviation respectively.