An isospin-dependent quantum molecular dynamical model (IQMD) is developed, with the isospin degree of freedom in the momentum-dependent interaction(MDI) included in IQMD, to obtain an isospin- and momentum-dependent interaction (IMDI) in IQMD. We investigate the effect of IMDI on the isospin fractionation ratio and its dynamical mechanism in the intermediate energy heavy ion collisions. It is found that the IMDI induces the significant reductions in the isospin fractionation ratio for all of beam energies, impact parameters, neutron-proton ratios and mass number of colliding systems. However, the strong dependence of isospin fractionation ratio on the symmetrical potential is preserved, with the isospin degree of freedom included in the MDI, i.e. the isospin fractionation ratio is still a good probe for extracting the information about the equation of state of isospin asymmetrical nuclear matter.