For the forward problem of excitation photon and emission photon in the fluorescent molecular tomography, which is usually solved in the sequential manner, a parallel algorithm which can simultaneously solve two forward diffusion equations is proposed. The algorithm realizes parallel computation through introducing multiplier matrix and decoupling the coupled equations. Two-dimensional numerical simulation is presented with the finite element method. Then the algorithm proposed is compared with the sequential method and the parallel algorithm proposed by Ralf B. Schulz et al.. Experimental results show that both the speed of the forward computation and precision of the forward solutions can be improved by using the proposed algorithm, which is adaptive to any Stokes shift and has more broad application. As a result, the whole process of fluorescent molecular tomography will also benefit from it.