Cognitive radio technology allows the secondary user to access channel from the spectrum range without interrupting the primary (licensed) user. This results in the changes of bottleneck bandwidth and RTT (Round Trip Time) during the channel switching. Hence TCP’s congestion window (cwnd) is updated using the protocol TCP CRAHN which have an issue in the throughput performance. To solve that issue, a new protocol TCP CoBA is used which updates the cwnd based on the buffer space in the relay node upon channel switching. This results in the increase of throughput performance. Existing research in transport protocols for wireless ad-hoc networks has focused on reliable end-to-end packet delivery under uncertain channel conditions, route failures due to node mobility and link congestion. In a cognitive radio (CR) environment, there are several key challenges that must be addressed apart from the above concerns. The intermittent spectrum sensing undertaken by the CR users, the activity of the licensed users of the spectrum, large-scale bandwidth variation based on spectrum availability, and the channel switching process need to be considered in the transport protocol design. This is achieved by adapting the classical TCP rate control algorithm running at the source to closely interact with the physical layer channel information, the link layer functions of spectrum sensing and buffer management, and a predictive mobility framework that is developed at the network layer. To the best of our knowledge, this is the first work on the transport layer to specifically address the concerns of the CR ad-hoc networks and our approach is thoroughly validated by simulation experiments.