The Diffuse Optical Tomography (DOT) is an in vivo optical imaging technique using scattered light to detect organization function with great range of depth. The most commonly used numerical method in solving its forward problem is finite element method (FEM). However, boundary element method (BEM) is a semi-analytic method, it is of higher computation accuracy, more effective for large scale problem than FEM since it only needs to discretize boundary which reduces the dimension of the problem. In this paper, we present a scheme of boundary element method for the diffuse light propagation in the heterogeneous medium. Comparing these calculations to Monte Carlo simulations, the results show a good agreement between both methods. BEM provides an optimization scheme for image reconstruction in DOT, and lay a foundation for the coupling of finite element method and boundary element method.