To eliminate the influence of profile on the extraction accuracy of optical characteristics of the tissue in spatial frequency domain (SFD) imaging, an SFD imaging correction method based on the target profile is proposed in this study. The method uses phase contour technology to obtain the three-dimensional (3D) profile of the target, and corrects the frequency and light intensity of the obtained SFD diffuse reflection image. The frequency correction adopts the optical characteristic interpolation method based on the multifrequency lookup table, and the correction of the incident and reflected light intensity is based on the law of illuminance and the Minnaert model. Experiments are performed using a single-pixel SFD imaging system based on a high-sensitivity phase-locked photon-counting detection technology, and a single-pixel imaging method based on two-dimensional(2D) discrete cosine transform is used to obtain topological images of the target profile and multiwavelength optical characteristics at low sampling rates. The experimental results show that the error of the target surface profile height at each pixel is not more than 1 mm, and the reconstructed absorption coefficient and reduced scattering coefficient after correction are reduced by 51.1 percentage points and 6.7 percentage points, respectively.