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It is open problem for the FAST TCP to estimate the true propagation delay. Aiming at the open problem, according to application characteristic of unilateral accelerated FAST TCP system, a novel two layers algorithm of the transport layer is proposed. In down layer, the history information of the active FAST TCP flows, such as the start-up time and the running time of FAST TCP flows, are gathered. When a new FAST TCP flow arrives, the upper layer algorithm can provide the current queue delay of the bottleneck link based on the earliest FAST TCP flow. For the first time in the calculation propagation delay, the down layer FAST TCP algorithm estimate the accurate propagation delay based on the current round trip delay minus the queuing delay provided by the upper algorithm. Finally, the NS-2 simulation results validate the effectiveness of this improved two layers algorithm.