A method is proposed to compensate intrinsic error in mirror symmetry absolute measurement. Because of the limitation of rotation times in mirror symmetry absolute measurement, intrinsic error of cNθ terms occurs in reconstructed wavefronts of three flats. By adding a rotation with a different angle, the wavefront difference between two measurements before and after rotation is calculated, and the Zernike coefficients of cNθ terms can be obtained by coefficient equations due to rotation invariability of the form of Zernike polynomials in polar coordinates. Therefore the intrinsic error of cNθ terms may be compensated. Because the amount of cNθ terms is infinite, the compensated terms are decided in terms of the balance between accuracy and computing capacity. Computer simulation proves the validity of the proposed method.