In this paper we have presented a numerical model to investigate the impact of the diffusion length of excitons and the layer thickness on the quantum efficiency of the organic bilayer solar cells. An organic solar cell composed of p3ht as the donor material and c60 as the acceptor and Al and ITO as the metallic electrodes is considered. Optical simulation is performed using FDTD method in order to obtain the electric field distribution and the absorption profile,then numerical modeling is performed by solving the exciton rate equation to calculate the quantum efficiency. Results shows that, although absorption efficiency increases with increasing thickness, quantum efficiency is decreased because of the limitation imposed by low diffusion length. Increasing the diffusion length of excitons leads more excitons to reach to the interface in their lifetime and consequently more free carriers are generated