Satellite Communication (SATCOM) systems are playing a more and more important role in both civilian and tactical scenarios with large deployment and user groups currently. However, long propagation delay and high packet loss rate of the SATCOM in higher earth orbits satellites degrades the communication performance severely. Existing works, such as Performance Enhancing Proxy (PEP), have addressed this performance issue via splitting the end-to-end TCP connection into several sub-connections, so that the low performance SATCOM communication link will no longer affect the entire TCP connection performance from the sender to the receiver. Nevertheless, PEP's functionalities can be disabled once the data encryption like High Assurance Internet Proto- col Encryption (HAIPE) was introduced due to the security requirement of the communication over SATCOM. Therefore, we targeted on the solution of using transportation layer tunneling, i.e., TCP and UDP tunnel, in this paper to explore the opportunity of re-enabling the PEP functionalities at the presence of data encryption and further enhancing the performance of the end-to-end TCP communication. We also designed and implemented a Mininet based emulation testbed to conduct all experiments and evaluations for better understanding on the effectiveness of the tunnel solution with different configurations (e.g., TCP congestion control mechanism). Based on the evaluation results presented in the paper, we successfully further improved the end-to-end TCP communication performance with TCP/UDP tunnel while maintaining the functionalities of the performance enhancement solution like PEP. Moreover, we provided detailed analysis on the advantages and disadvantages of using different tunnels with different configurations as well as our recommendations for performance enhancement in such SATCOM communication environment.