For the container terminal, the berth scheduling is an important task that affects the terminal operations, and the berth allocation is the primary matter. In order to reveal the degree of influence of berth preference to the results of berth allocation, two aspects including the berth allocation and the influence of preference are studied. In order to optimize both the berth allocation and maximize the preference of berth, a multiobjective mixed integer linear mathematical model under the constraints of the preference for berth is presented. CPLEX is used to solve the model. The efficiency of the model is demonstrated by the experiments, and the effects of berth preference are analyzed. The results are beneficial for the operations of container terminals, and new features are introduced for discrete the berth allocation problem.