This paper describes a new scheduling solution for large number multi-product batch processes with complex intermediate storage system. Recently many batch chemical industries have turned their attention to a more efficient system known as a pipeless batch system. But existing plants need to change their systems to pipeless systems, piece by piece. In this case, current systems are changed to pipeless systems by way of non critical process operations such as through the use of intermediate storage. We have taken the conventional batch plant with a pipeless storage system as an objective process. Although the operation of a pipeless storage system becomes more complex, its efficiency is very high. With this system, all of the storage should be commonly used by any batch unit. For this reason, solving the optimal scheduling problem of this system with a mathematical method is very difficult. Despite the attempts of many previous researches, there has been no contribution which solves the scheduling of intermediate storage for complex batch processes. In this paper, we have developed a hybrid system of heuristics and Simulated Annealing (SA) for large multi-product processes using a pipeless storage system. The results of this study show that the performance and computational time of this method are superior to that of SA and Rapid Access Extensive Search (RAES) methods.