The integrating optimization of resource allocation and operation scheduling in the main operation area of the railway container terminal has a significant impact on operation performance and efficieny. Based on the gantry cranes and trucks cooperative handling plan and introducing the principle of dynamic allocation of gantry cranes, a multi-objective non-linear mixed-integer programming model is constructed, which is to maximize balance rate and minimize handling costs, to comprehensively study the multi-level collaborative optimization problems, including the crane area division, slot assignment, and multi-gantry crane scheduling. Based on the characteristics of the problem, combining the heuristic rules, the genetic algorithm, and the simulated annealing algorithm, a three-layer hybrid heuristic algorithm is designed to solve the model. The Cplex solver and the algorithm designed are applied to solve different scale examples to verify the correctness of the model and the effectiveness of the algorithm. By comparison with the experimental results of different division principles, optimization strategies, and interval constraints, the universality of the model and algorithm are shown. The results show that the new handling scheme, dynamic crane area, and the integrating optimization strategy can greatly balance the rate of gantry crane operation, avoid overburdening resources and reduce the handling cost of the railway container terminal, which provides decision support for the actual operation and management of it.