As a new type of part-to-picker storage system, the double-deep multi-tier shuttle system has been developed rapidly in the e-commerce industry because of its high flexibility, large storage capacity, and robustness. The system consists of a multi-tier shuttle sub-system that controls horizontal movement and a lift sub-system that manages vertical movement. The combination of shuttles and lifts, instead of a stacker crane in conventional automated storage and retrieval system, undertakes inbound/outbound tasks. Because of the complex structure and numerous equipment of the system, task scheduling has become a major difficulty in the outbound operation of the double-deep multi-tier shuttle system. Figuring out methods to improve the overall efficiency of task scheduling operations is the focus of current system application enterprises. This paper introduces the task scheduling problem for the shuttle system. Inspired from workshop production scheduling problems, we minimize the total time of a batch of retrieval tasks as the objective function, applying the modified Simulated Annealing Algorithms (SAAs) to solve the task scheduling problem. In conclusion, we verified the proposed model and the algorithm efficiency, using case studies.