With time-based competition and rapid technology advancements, effective manufacturing scheduling and supply chain coordination are critical to quickly respond to changing market conditions. These problems, however, are difficult in view of inherent complexity and various uncertainties involved. Based on a series of results by the authors, decomposition and coordination by using Lagrangian relaxation is identified in this paper as an effective way to control complexity and uncertainty. A manufacturing scheduling problem is first formulated within the job shop context with uncertain order arrivals, processing times, due dates, and part priorities as a separable optimization problem. A solution methodology that combines Lagrangian relaxation, stochastic dynamic programming, and heuristics is developed. Method improvements to effectively solve large problems are also highlighted. To extend manufacturing scheduling within a factory to coordinate autonomic members across chains of suppliers, a decentralized supply chain model is established in the second half of this paper. By relaxing cross-member constraints, the model is decomposed into member-wise subproblems, and a nested optimization structure is developed based on the job shop scheduling results. Coordination is performed through the iterative updating of cross-member prices without accessing other members’ private information or intruding their decision-making authorities, either with or without a coordinator. Two examples are presented to demonstrate the effectiveness of the method. Future prospects to overcome problem inseparability and improve computing efficiency are then discussed.