The accuracy of the background optical properties has a considerable effect on the quality of reconstructed images in near-infrared functional brain imaging based on continuous wave diffuse optical tomography (CW-DOT). We propose a region stepwise reconstruction method in CW-DOT scheme for reconstructing the background absorption and reduced scattering coefficients of the two-layered slab sample with the known geometric information. According to the relation between the thickness of the top layer and source–detector separation, the conventional measurement data are divided into two groups and are employed to recon-struct the top and bottom background optical properties, respectively. The numerical simulation results demonstrate that the proposed method can reconstruct the background optical properties of two-layered slab sample effectively. The region-of-interest reconstruction results are better than those of the conventional simultaneous reconstruction method.