Based on the full analysis of the whole process of intercity travel of urban agglomerations, a super network model of urban agglomeration intercity multi-mode traffic system is constructed. The super network link is divided into travel link, transfer link, boarding link and alighting link, in which the travel link includes the travel link on the urban transportation network and the travel link on the intercity transportation network. Considering the factors of travel time, cost and degree of comfort, the generalized cost function and generalized hyper-path cost function are established for all links. On the basis of this, the stochastic equilibrium assignment model of urban agglomeration intercity multi-modal transportation system is proposed and the corresponding algorithm is designed based on MSA algorithm. Finally, an example is presented to illustrate the proposed method.