With the trend of terminal automation and the requirement for port operation efficiency to be greatly improved, it is very necessary to optimize the traveling route of automatic guided vehicles (AGV) with reference to the connection of loading and unloading equipment. As a complex multi-equipment system, it is inevitable that AGV will collide when traveling due to various accidents in actual operation, which will lead to AGV locking and reduce the efficiency of terminal operation. Considering the locking problem of AGV, we propose a three-stage integrated scheduling algorithm for AGV route planning. Through joint optimization with quay cranes (QC) and yard blocks, a road network model is established in the front area of the container port to optimize the path of AGV in the road network, and a speed control strategy is proposed to solve the problem of AGV collision avoidance. In the first stage, we establish the AGV optimal route model with the goal of minimizing the AGV path according to the AGV road network situation. In the second stage, on the basis of the determination of AGV route planning, and when the container task is known, the AGV task assignment model is established with the goal of minimizing the maximum completion time, and the model is solved by genetic algorithm (GA). In the third stage, on the basis of AGV task assignment and route determination, the AGV route and AGV task assignment scheme are input into the simulation model by establishing the AGV collision avoidance control model for speed control, and establishing the AGV route network simulation model for automated terminals considering collision avoidance in plant simulation software. The maximum completion time obtained from the simulation model is compared with the completion time obtained from the genetic algorithm. The proposed three-stage joint scheduling algorithm can improve the loading and unloading efficiency of the port, reduce the AGV locking situation, and has a certain contribution to the formulation of the actual operation planning of the port.