The invention relates to a flow scheduling system and method based on SDN. The method comprises the following steps: acquiring a network link parameter configured by a user; starting routing collection and flow collection processes; performing link analysis; judging whether a congested link exists, if so, scheduling the flow of the congested link to an idle link by a flow scheduling module, and otherwise, continuing to perform periodic link analysis. By adoption of the system and the method, being different from the system under distributed architecture, the flow scheduling method and system based on the SDN can comprehensively sense the link congestion or link faults; the network link heath condition updated in real time can be converted to a network link metric coefficient, and thus the selection of an optimal path is more accurate; and in the case of network link congestion, the flow scheduling method and system based on the SDN provided by the invention are started to quickly and effectively eliminate the link congestion, and the links are reasonably configured to maximize the bandwidth utilization rate, and flow load balance of the whole network can be realized.