In order to improve the adaptability of scheduling strategy to the change of the arrival density of the workpiece, the dynamic scheduling method in flexible job-shop was studied. Firstly, the dynamic scheduling system of flexible manufacturing based on multi-agent system is constructed according to the investigation results and agent modeling method. And combining with the complex structure processing characteristics of flexible manufacture, the operation mechanism of scheduling task decomposition, machine tool selection and task allocation is improved, and forming the task decomposition mechanism based on the process, machine tool selection mechanism based on the machining accuracy and dynamic time windows scheduling method based on scheduling rules. Finally, the feasibility of the proposed dynamic scheduling method in the scenario of work-piece density change is verified by experiments, which has a certain guiding significance for the current actual flexible job-shop production activities.