The aim of this study is to construct a new model to measure the supply and demand non-equilibrium of transportation system, which is more accuracy and effect compared to the traditional model. Based on the non-equilibrium problem of supply greater or less than demand, which is common in current city agglomeration transportation system, the supply and demand non-equilibrium depth of city agglomeration transportation system is proposed. From the perspective of the connotation of supply and demand non-equilibrium depth of city agglomeration transportation system, the category is definitely divided, and then the corresponding functions of supply and demand of the city agglomeration transportation system are established. According to the interaction mechanism of the supply and demand of the city agglomeration transportation system, the non equilibrium depth in a narrow and general sense can be calculated respectively, also the total non-equilibrium depth is obtained, containing its three-dimensional structure and the fitting surface. In the case study, it is indicated that the research conclusion meets the actual requirements completely.