Reasonable scheduling of a train’s loading and unloading equipment can reduce the energy consumption of production operations; this has great value for the green development of terminals. The collaborative scheduling model of the Automated Rail Mounted Gantry (ARMG) and Automated Guided Vehicle (AGV) is used to minimize the energy consumption of equipment in a scenario of a vertical railway entering a port and a shared storage yard existing between the port and railway under the mixed operation mode of “train–ship” and “train–yard–ship”. According to the characteristics of the model, the two-layer scheduling rule and the self-adaptive chaos genetic algorithm (SCGA) were proposed to solve the problem of placing the ARMG and the AGV on the same schedule. Simulation experiments verified the effectiveness of the model and algorithm. The effects of the delayed arrival of vessels, the proportion of “transshipment” containers, and the number of automated ARMGs and AGVs on total energy consumption were analyzed. The results showed that when all containers are “train–ship” containers, the number of ARMG and AGV at 1:4 will minimize the total operational energy consumption. Furthermore, as ships take longer to arrive, reducing the number of AGVs can cut energy use by 15% for the same number of ARMG.