The cognitive mobile ad hoc network is considered as a promising solution for the scarcity of wireless resources. The performance of the transport layer is degraded due to the cognitive radio characteristics like spectrum sensing and spectrum switching. This paper discusses the effects of cognitive operations on the classical TCP. A comparison between the existing transport layer protocols limitations and performances under the cognitive networks circumstances is introduced. Also, this paper proposes a flow control during the channel switching. A feedback acket to enhance the performance of TCP during the sensing period. Improvement in the throughput of the proposed protocol is shown in simulation results.