The focus for the current freight reform of national railway is to break down the boundaries not only between railway bureaus but also between railways and ports, thus dredging the regional railway freight channels and cutting down the energy consumption and the carbon emissions of rail freight. The profit allocation method is the key among various influencing factors for forming regional alliance of railway freight. Taking into account the irrationality during the profit allocation of regional alliance of railway freight, this paper firstly constructed a mathematical programming model based on the least square method, then solved the quadratic programming model to determine players’ imputations after the cooperation. Finally, a numerical example was given to show the applicability and advantages of the model and the proposed method.