Integrated and coordinated decision-making across various value chains and levels of decision-making is one of major goal in process systems engineering. To ensure more sustainable and robust decision-making, effective integrated operation and optimization methodologies for multi-scale system is needed. Case studies on multi-time scale systems, which are oil refinery and industrial shipping respectively, are conducted in this study. In first case study, integrated operation between procurement planning and production scheduling in oil refinery is discussed. Alternative to the complete mathematical operation of two systems, two systems are closely related by quantifying effects of each crude on the gross margin of system, and apply them as weight parameters in objective function of procurement planning problem. In second case study, integration between tramp liner rental planning and vessel dispatch scheduling in industrial shipping system is discussed. Shipping problem is formulated in MP/MDP (mathematical programming/Markov decision process) combined structure where vessel dispatch scheduling problem is formulated in MP and tramp liner rental planning is formulated in MDP. The computability of scheduling MP is improved by simplified MILP with heuristic schedule decision, and MDP is solved by approximate dynamic programming (ADP) by linear value function approximation where basis function of approximated value function are selected by analysis of variance (ANOVA). Formulation and methodologies at two cases studies are simulated with historical operation data of each system.