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.