There is a shared problem in current optical imaging technologies of how to obtain the optical parameters of biological tissues with complex profiles. In this work, an imaging system for obtaining the optical parameters of biological tissues with complex profile was presented. Firstly, Fourier transformation profilometry was used for obtaining the profile information of biological tissues, and then the difference of incident light intensity at different positions on biological tissue surface was corrected with the laws of illumination, and lastly the optical parameters of biological tissues were achieved with the spatial frequency domain imaging technique. Experimental results indicated the proposed imaging system could obtain the profile information and the optical parameters of biological tissues accurately and quickly. For the slab phantoms with height variation less than 30 mm and angle variation less than 40º, the maximum relative errors of the profile uncorrected optical parameters were 46.27% and 72.18%, while the maximum relative errors of the profile corrected optical parameters were 6.89% and 10.26%. Imaging experiments of a face-like phantom and a human’s prefrontal lobe were performed respectively, which demonstrated the proposed imaging system possesses clinical application value for the achievement of the optical parameters of biological tissues with complex profiles. Besides, the proposed profile corrected method can be used to combine with the current optical imaging technologies to reduce the influence of the profile information of biological tissues on imaging quality.