The recent manufacturing environment is characterized as having diverse products due to mass customization, short production lead-time, and unstable customer demand. Today, the need for flexibility, quick responsiveness, and robustness to system uncertainties in production scheduling decisions has increased significantly. In traditional job shops, tooling is usually assumed as a fixed resource. However, when tooling resource is shared among different machines, a greater product variety, routing flexibility with a smaller tool inventory can be realized. Such a strategy is usually enabled by an automatic tool changing mechanism and tool delivery system to reduce the time for tooling setup, hence allows parts to be processed in small batches. In this research, a dynamic scheduling problem under flexible tooling resource constraints is studied. An integrated approach is proposed to allow two levels of hierarchical, dynamic decision making for job scheduling and tool flow control in Automated Manufacturing Systems. It decomposes the overall problem into a series of static sub-problems for each scheduling window, handles random disruptions by updating job ready time, completion time, and machine status on a rolling horizon basis, and considers the machine availability explicitly in generating schedules. Two types of manufacturing system models are used in simulation studies to test the effectiveness of the proposed dynamic scheduling approach. First, hypothetical models are generated using some generic shop flow structures (e.g. flexible flow shops, job shops, and single-stage systems) and configurations. (Insup Um, Hyeonjae Cheon, Hongchul Lee, 2009; Stefan Bock, 2008). They are tested to provide the empirical evidence about how well the proposed approach performs for the general automated manufacturing systems where parts have alternative routings. Second, a model based on a real industrial flexible manufacturing system was used to test the effectiveness of the proposed approach when machine types, part routing, tooling, and other production parameters closely mimic to the real flexible manufacturing operations.