Berths and quay cranes are scarce resources in the container terminal system. If the equipment is reasonably planned, the service quality might be improved and the operation cost of the terminal would be reduced. In addition, the competition among ports is not only the competition of the terminal service quality, throughput, and scale but also the competition of low-energy consumption and low pollution. In order to reduce carbon dioxide emissions, this paper developed a multiobjective optimization model for the joint allocation of container terminal berths and Quay cranes. The model is developed based on preference of ships for berths, and the impact of carbon emission cost on terminal operations have been considered. The carbon cost from two aspects, namely, reducing the operation cost of ships and minimizing the average waiting time and departure delay of ships, has been considered. The improved adaptive genetic algorithm has been used to solve the model. A container terminal in Ningbo has been used as a case study. The carbon emission cost of the berths and quay cranes operation system has been calculated. The influence of the variation in carbon emission cost on the berths and quay cranes configuration scheme has been evaluated. The result proves that considering the carbon cost can make the berths and quay cranes operation more green and reasonable. It can be seen that the objective function value of the joint scheme is 5.92% lower than that of the traditional scheme, and the terminal operation cost of carbon emission constraints is 11.76% lower than that of no carbon emission constraints.