The work aims to improve the operation efficiency of the double-loading multi-shuttle automated storage and retrieval system (DMS/RS) and studies its slotting optimization. With respect to the characteristics of slotting optimization operation of DMS/RS, considering the acceleration (deceleration) characteristics during the motion, the optimization model of slotting allocation aiming at the shortest warehousing time was constructed. A hybrid plant propagation algorithm combined with the crossover and mutation operator was designed for the optimization solution of the model, thus determining the best slotting allocation plan and shortening the slotting allocation time. The instant analysis showed that, the convergence speed was faster and the optimization efficiency was higher compared with the genetic algorithm and plant propagation algorithm. The hybrid plant propagation algorithm can effectively shorten the slotting allocation time of the DMS/RS and improve the operation efficiency of warehouse.