One of the key targets for LTE/SAE is 100 Mbps peak data rate in downlink. While compared to the lined data rate, the wireless data rate is still a bottleneck. This means if there is no flow control in aGW; packets will be buffered in eNB. While the buffer in eNB is limited, packets may be dropped. To reduce the harm to the performance of the TCP based application from packet loss, flow control is needed. There are huge amount of flows in one eNB and the rate varies from 10 kbps to 10 0Mbps. In addition, the radio channel has the time-varying nature. All of them produce the challenge to the flow control of LTE/SAE. This paper proposes the hierarchy virtual queue (HVQ) based flow control mechanism to solve the problems. Simulation results show HVQ flow control requires fewer resources but produces better system performance.