In view of the trend of upsizing ships, the physical limitations of natural waterways, huge expenses, and unsustainable environmental impact of channel widening, this paper aims to provide a cost-efficient but applicable solution to improve the operational performance of container terminals that are enduring inefficiency caused by channel traffic limitations. We propose a novel berth scheduling problem considering the traffic limitations in the navigation channel, which appears in many cases including insufficient channel width, bad weather, poor visibility, channel accidents, maintenance dredging of the navigation channel, large vessels passing through the channel, and so on. To optimally utilize the berth and improve the service quality for customers, we propose a mixed-integer linear programming model to formulate the berth scheduling problem under the one-way ship traffic rule in the navigation channel. Furthermore, we develop a more generalized model which can cope with hybrid traffic in the navigation channel including one-way traffic, two-way traffic, and temporary closure of the navigation channel. For large-scale problems, a hybrid simulated annealing algorithm, which employs a problem-specific heuristic, is presented to reduce the computational time. Computational experiments are performed to evaluate the effectiveness and practicability of the proposed method.