In order to realize the efficient utilization of space-time resource in port station yard, the distribution trains organization scheme is studied. The paper considers sea-rail combined transport operation links after ships arrive at the port. When the arrival time of ships is definite, the optimization model of distribution trains organization scheme is established. The model with the goal of minimizing the product of total container storage quantity and storage time in the port station yard. The model considers constraints such as the loading capacity of distribution trains, the storage capacity of the port station yard, the shortest departure time interval in the port station and so on. On this basis, another optimization model is established that the arrival time of ships is fuzzy by using chance constraint theory. Finally, a case is designed to verify the effectiveness of the model. The sensitivity analysis of the average loading time of a single container in the port station is carried out. The results show that shortening the parameter affects the organization scheme, which can reduce the value of objective function. The method provides support for the compilation of the distribution trains organization scheme in the port station.