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We investigate the role of isospin momentum-dependent interaction on the isospin fractionation ratio and its dynamical mechanism in the intermediate energy heavy ion collisions, by inserting an isospin degree of freedom into the momentum-dependent interaction to obtain an isospin momentum-dependent interaction given in a form practically usable in the isospin-dependent quantum molecular dynamics model It is found that the isospin momentum-dependent interaction brings an important isospin effect into the isospin fractionation ratio. In particular, the isospin momentum-dependent interaction reduces obviously the reduction of isospin fractionation ratio. Thus the isospin dependence of momentum-dependent interaction is thus important for studying accurately the equation of state of isospin asymmetry nuclear matter.