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The bundle protocol (BP) is developed to solve the new problems in deep space exploration. To date, little work has been done in evaluating the performance of BP applied to an interplanetary Internet involving frequent link disruptions. This paper builds a PC-based Deep Space Communication Test-bed. It consists of three parts, the space link simulator, the high-speed Ethernet switch and the Linux-based personal computers. Compared with the simulation in OPNET, NS2 and other simulation software, the experimental results from the Test-bed will be closer to the real environment. The paper presents an experimental evaluation of BP over a typical three-node interplanetary structure involving frequent link disruptions. The performances were analyzed to compare the throughput of BP with custody transfer and BP without custody transfer under the various scenarios. The results show that BP without custody performs better than BP with custody in a cislunar environment.