Acquisition of the optical structures within a biological body is critical to all the diffuse light imaging modalities, such as diffuse optical tomography(DOT) and fluorescence molecular tomography(FMT). On an assumption of the optical homogeneity within the organs, it can be cast as a shape-based DOT issue, which aims to simultaneously recover the smooth region boundaries and optical properties of the biological tissue. The boundary element method (BEM) is used for the forward modeling and implemented in two dimensions, and compared with those obtained from the finite element method (FEM) approach for the validation. A truncated singular value decomposition(truncated-SVD) optimization method is implemented for the inverse problem, which is evaluated in a domain with 3 heterogeneous inclusions at 40 dB noise level. The numerical simulations show that the methodology is very promising and of good convergence. The shape parameters and the optical coefficients can be reconstructed with good accuracy at a reasonable noise level.