Combined-mode traffic assignment is one of the key links for multi-modal transportation planning. In order to quantitatively evaluate the implementation effect of combined-mode transportation and explore its assignment mechanism, a combined-mode traffic assignment model with travel constraints is proposed. First, the practical factors of combined mode in real world are discussed and integrated into the analysis of multi-modal network transformation as related constraints. Second, the physical transportation network is translated to equivalent super network (SN) and state-augmented network (SAN) based on the graph theory. Moreover, the network size constrained by the actual conditions is conducive to further analysis of combined-mode trips. Third, a tri-level combined-mode traffic assignment model is formulated based on the simulation platform of SAN. The first level of the model is to address the combined-mode choice, the second level is to transfer choice on SAN, and the third level is to characterize auto travelers’ route choice behavior. By analyzing the impedance in multi-level network, an MSA algorithm solving Nest-Logit model is proposed. Finally, numerical example is performed to validate the model. The method proposed in this paper considers the travel similarity, reduces the network scale, conforms to the travel logic and makes up for the shortcomings of traditional traffic allocation methods.