An isospin degree of freedom is inserted into the momentum dependent interaction in the quantum molecular dynamics model to obtain an isospin dependent momentum interaction given in a form practically usable in isospin dependent quantum molecular dynamics model. We investigate the entrance channel effects for the role of isospin momentum dependent interaction on the isospin fractionation ratio and its dynamical mechanism in the intermediate energy heavy ion collisions. It is found that the isospin dependent momentum interaction induces a significant reduction of isospin fractionation ratio under all entrance channel conditions. However the strong dependence of isospin fractionation ratio on the symmetry potential is preserved after considering the isospin degree of freedom in the momentum dependent interaction.