A measurement system for on-line determination of optical properties of tissue with large areas and correction of complex surface profile was developed. First, the three-dimensional surface profile of the tissues was obtained with phase profilometry. According to cosine radiator model, the change of illumination, which was caused by complex surface profile of the tissues, was corrected. Then, diffuse plane was used to replace the phantom in the traditional method, and the absolute optical parameters based on spatial frequency domain measure mode were measured. The absorption coefficient of the tissues was reconstructed using the developed method. Tissues phantoms with height variation less than 29 mm were adopted to verify the method, the relative error of absorption coefficient decreased from 60% to 13% compared to that without correction.