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From the angle of whole trip chain, the paper constructs the passenger flow assignment model in comprehensive transportation network based on the general cost equilibrium through full consideration of the passengers' trip behavioral characteristics. In this model, it is proposed that connection and transfer efficiency among the different transportation modes and urban traffic modes in distribution nodes should be taken into account, whose quantization method and mathematical network transformation method of general cost are also proposed. To solve the model, general cost-flow function is firstly constructed based on different modes and connection-transfer system through considering the links' controlling modes and managing characteristics and the assignment result is obtained through applying the iteration method of all-or-nothing. Finally, the comparative analysis is carried out through taking the comprehensive transportation networks in the Guanzhong-Tianshui economic area as a case to prove the model's validity and Practicality.