In order to study the impacts of berthing priority of shore power ships and time-of-use price on scheduling of berths and quay cranes. A nonlinear mixed-integer planning model was constructed for the joint dynamic scheduling of berths and quay cranes with the goal of minimizing the total cost of ships and carbon emissions. The non-dominated sorting genetic algorithm Ⅱ(NSGA-Ⅱ) was improved by two-population co-evolution and the adaptive operators of crossover and mutation to solve the model, and the effectiveness of the improved algorithm was verified. The results show that the solution effect of improved NSGA-Ⅱ is better than that of NSGA-Ⅱ. Under time-of-use price, the berthing priority for shore power ships can effectively reduce the cost of shore power ships and improve the enthusiasm of no shore power ships to retrofit and use shore power. The bigger the gap between the electricity price of peak and low period is the higher the cost of shore power ships and the lower the carbon emission and the cost of no shore power ships. More shore power ships do not give priority to berthing to avoid the electricity price of peak period. The results of the study can provide a scientific basis for the development of reasonable scheduling scheme under the policy of berthing priority and time-of-use price for shore power ships.