The freight traortation system plays an important and influential role in the national economy, which also systematically influences numerous parts of society. To the better achievement of efficient freight planning, we want to model a sustainable rail-based intermodal hub location problem based on the network planner perspectives and cargo owner preferences. In this thesis, we present the objective function as the network planner environmental perspective and specific constraints reflecting cargo owner preferences for choosing different modes of traortation. Cargo owner preferences comprise two primary criteria of time and cost for shipping cargoes via different traortation modes. Stated preference (SP) data is used to reflect cargo owner preferences into a time-cost graph. According to the cargo owner mode choice reflection on the time-cost graph, we estimate a mathematical line and seven bounds to distinguish cargo owner reaction to time and cost. As stated by the budget levels, our network planner can perform different approaches like building new hubs and also new links to consider these approaches impacts on the freight planning structure within the hub-based network. Budget levels and economy of scale change impacts on the produced and also, traortation mode shares are analyzed. Our proposed model is solved precisely by the GAMS software for chosen candidate nodes of Iran rail-road network.