A method for controlling transmission data flow in a satellite communication system is disclosed. The current status is notified to a main board of a central station and to a main board of a terminal station in accordance with the flow control buffering status of a satellite communication board of the central station, and thus, the main board of the central station commands a starting or a releasing of a flow control to a subscriber board of the central station. In accordance with the flow control buffering status of the subscriber board of the central station, its status is notified to the main board of the central station, so that the main board of the terminal station can start or release the flow control. In accordance with the flow control buffering status of the main board of the terminal station, its status is notified through a satellite communication board of the central station to the main board of the central station, so that the subscriber board of the central station can start or release the flow control. Thus the system grounding-down due to the flow controls of the network factors and due to the user data rush is prevented.