In this paper, a generic and flexible optimisation methodology is developed to represent, model, solve and analyse the iron ore supply chain system by integrating of iron ore shipment, stockpiles and railing within a whole system. As a result, an integrated train-stockpile-ship timetable is created and optimised for improving efficiency of overall supply chain system. The proposed methodology provides better decision making on how to significantly improve rolling stock utilisation with the best cost-effectiveness ratio. Based on extensive computational experiments and analysis, insightful and quantitative advices are suggested for iron ore mine industry practitioners. The proposed methodology contributes to the sustainability of the environment by reducing pollution due to better utilisation of transportation resources and fuel.