Embodiments of the present invention provide a congestion control method and apparatus based on a software defined network SDN, and an SDN controller. The method comprises: obtaining a packet_in message sent by a switch; determining a data packet included in the packet_in message; performing a first congestion control processing for a network where the SDN controller is located based on a topological structure and link information of the network when the data packet is a handshake information SYN packet for requesting to establish a TCP connection; performing a second congestion control processing for the network based on the link information when the data packet is a finish information FIN packet for responding to disconnection of a TCP connection; deleting information of a TCP connection stored in a database and corresponding to the data packet when the data packet is an FIN packet requesting to disconnect a TCP connection. As compared with the prior art, by using the solutions according to the embodiments of the present invention, the SDN controller may improve fairness of the bandwidth between each data flow, and reduce TCP retransmission and timeout caused by the highly burst short traffic, and achieve the control of the TCP Incast congestion existing in the datacenter.