Supply chain management is the key to the success and playing a large role in the modern world in every manufacturing and service sector. The effectiveness of the material handling system has a valuable impact on the excellence of supply chain. Although this is a non-value adding process but, can’t be avoidable. Therefore, it is required to minimize the cost, time and effect of the material handling system. To analyse and simulate the MHS, port container terminal operations are taken in to study. Every operation in the CT is handling the material. In order to perform the effective handling, storage and retrieval at the stack is very much important. To execute the effective system, it is required to analyse the different scenarios such as various layouts and change of operations using mathematical modelling and Simulation techniques. These results of the different scenarios are compared for the efficiency of the stack.