The container terminal system is a complex production system which is composed of many subsystems, and the equipment scheduling in the system is also a complex problem which involves a variety of uncertainties. The probability distribution of equipment operation parameters was considered emphatically, and the coordinated scheduling problem between quay crane and yard truck was studied. The method of multidisciplinary variable coupling design optimization with time window constraint was presented, the yard truck distribution sub-model and yard truck configuration sub-model were built. Completion time and the number of trucks were regarded as public design variables to connect the two submodels, and the coupling model for coordination scheduling was established. This model selected data from a terminal of Shanghai port, and called Gurobi4.0 to solve the coupling model under the environment of Visual studio2012. Compared the final scheduling project with the original project, the cost of total delay time decreased by 90.69%, and the number of container trucks decreased by 30.76%, which shows that the model is effective and practical.