The integrated allocation and scheduling of handling resources are crucial problems in the railway container terminal (RCT). We investigate the integrated optimization problem for handling resources of the crane area, dual-gantry crane (GC), and internal trucks (ITs). A creative handling scheme is proposed to reduce the long-distance, full-loaded movement of GCs by making use of the advantages of ITs. Based on this scheme, we propose a flexible crossing crane area to balance the workload of dual-GC. Decomposing the integrated problem into four sub-problems, a multi-objective mixed-integer programming model (MIP) is developed. By analyzing the characteristic of the integrated problem, a three-layer hybrid heuristic algorithm (TLHHA) incorporating heuristic rule (HR), elite co-evolution genetic algorithm (ECEGA), greedy rule (GR), and simulated annealing (SA) is designed for solving the problem. Numerical experiments were conducted to verify the effectiveness of the proposed model and algorithm. The results show that the proposed algorithm has excellent searching ability, and the simultaneous optimization scheme could ensure the requirements for efficiency, effectiveness, and energy-saving, as well as the balance rate of dual-GC.