Theoretical model has been derived in the electrophoretic separation system where an electric potential is applied to the system in the axial direction. The effect of electrophoretic convection in the polymeric media is significantly contributed to separate large ionic-molecules because the conformation of large ionic-molecule quickly orients in the field direction. The dependence of the transport in the polymeric media upon field intensity and molecular size aids in understanding the transport of large ionic-molecule in the system, since the convective velocity of large ionic-molecule is accelerated inside a porous material. The separation of two different large ionic-molecules is predicted with a value of $(Pe_t/Pe_g)$ of individual large ionic-molecule using an operator and the reptation theories.