The invention provides a workflow operation method and a system thereof. The method comprises the steps: presetting a flow definition model and a flow operation model, wherein the flow definition model comprises preset task definition, flow definition, node and migration objects, the flow operation model comprises preset flow instance, flow branch, task instance and flow variable objects; creating a flow instance according to the preset flow definition, and creating an execution thread corresponding to the flow instance; triggering the execution thread to flow, so as to acquire migration flow direction of a left flow at an initial node of the flow instance; and calling the migration flow direction of the flow to trigger workflow to operate. The method and the system provided by the invention can firstly meet workflow operation requirements of high data quantity and high concurrent load, secondly reduces application difficulty of development, testing and management, and finally has simple technical architecture and low hardware requirement while meeting performance requirement and also meets the low cost intensification requirement.