During the last years, the requirements on logistics increased due to the fast growth in progressive markets like China and the trend of industries towards a customer order-related production. Properly designed and controlled supply chain networks gain more and more importance. All parts of the supply chain must be effectively connected and structured to ensure competitiveness. Therefore, the management of complex value chains and material flows is getting more important. There is an obvious deficit of literature on the control of material flows in process industries. This dissertation thesis contributes to the further development of this research field. After commonalities and distinguishing properties in typical material flow systems are identified, we categorize their complexity, drivers and propose methods to diminish, avoid or handle complexity. Subsequently, the effects of complexity drivers on costs are presented. An innovative method to evaluate complexity in the operational production area, especially regarding order sequence planning issues is developed and tested in a real world scenario. This evaluation is a practical approach to consider the factor complexity within the production planning and control process. Enterprises can utilize this method to evaluate complexity in the production process and develop methods accordingly.