This paper analyzed the hinterland of the inland river ports connected with the discrete highway network. Therefore, the dense hinterland transportation network and the sparse highway network, together with the inland waterway system, form a continuous-discrete multi-modal freight transportation system. We proposed an aggregate model to capture the shippers’ joint route and port choice behavior with the mixed logit model. We compared the hinterland topologic structures with and without discrete highway network and investigate the utilization of the highway network in the continuous-discrete multi-modal freight transportation system. The proposed model is adopted to examine the hinterland topologic structure of the inland river ports located in the Yangtze River Economic Belt.