The invention provides a flow control method and system based on SDN configuration, and the method comprises the steps: an SDN switcher detects a receiving and transmitting buffering region, and obtains a flow causing the overflowing of the receiving and transmitting buffering region when the overflowing of the receiving and transmitting buffering region is detected; the SDN switcher extracts the flow characteristic code of the flow, and transmits the flow characteristic code to an SDN controller; the SDN controller obtains the transmitting path of the flow according to the flow characteristic code, and transmits a flow table containing flow control instruction information to a source end switcher, generating the flow, according to the transmitting path; and the source end switcher stops or stops the transmitting of the flow temporarily according to the control instruction information specified by the flow meter. The method and system can positioning the flow which causes the overflowing of the receiving and transmitting buffering region, and can stops the inputting of the flow when the follow enters into a network source end, thereby preventing frame loss during the blocking of a port, and guaranteeing the stability of a user network.