This paper aims to study the route optimization problem for compound operations of the Shuttle-Carrier Warehousing System (SCWS), which is favorable to improve the operation efficiency and reduce the cost of the system. The actual scheduling route of SCWS in three kinds of different operating modes were analyzed in a couple of access operation; and the mathematical model with the goal of the shortest time to access the cargo was established by considering the acceleration and deceleration during the motion. According to the characteristics of compound operations in the system, a hybrid particle swarm algorithm combining ant colony algorithm and crossover and mutation operator was designed to optimize the model. The analysis result showed that compared with particle swarm and ant colony algorithm, the proposed hybrid particle swarm had more stable performance and higher optimization efficiency. The method proposed in the paper can effectively shorten the time of compound operations of the shuttle-carrier warehousing system to improve the efficiency of the loading/unloading scheduling.