Abstract : Acquiring knowledge about space has fascinated humans since the antiquity. Since a few decades, there is a significant increase in space mission programs like Mars and Lunar Exploration Missions, and Spatial exploration projects become more and more complex, involving several different communicating nodes: satellites, robots (Rovers, Landers) or "aerorobots" (i.e. atmospheric sensors). To this extend, efforts have been made by the space standardization bodies such as the Consultative Committee for Space Data Systems (CCSDS) and the Delay Tolerant Networking working group within the Internet Research Task Force (IRTF) to develop effective protocol architecture for space missions. In this dissertation, we have analyzed various newly proposed protocol stack (CCSDS, DTN) for their performance over Interplanetary Network and derived the parameters which affect the performance of the system, like buffer storage, power limitation, also explored various networking issues in routing, transport & application layers of the protocol stack, which is to be addressed. To that extend, in this thesis we have proposed a Resource Aware routing protocol, which uses knowledge about the connectivity, resource consumption of the nodes and buffer management policy to make an effective routing decision to route all kind of traffic in interplanetary network, where communicating entities are of different natures. Since there are various interoperable protocols proposed by space agencies, we then developed a QoS framework, which help the interplanetary applications to choose optimum underling protocols (Transport), suitably measured in term of ability to achieve the application QoS requirements with the environmental, constrains. As the analysis shows that the performance CCSDS File delivery protocol which is most commonly used application protocol in space mission, depends on the preset timeout value of its timer due to varying propagation delay. To improve the performance of the protocol, in out thesis we have developed a dynamic timer algorithm which sets the timeout values according to network condition for all the timers in the protocol, in a way that reduces unnecessary retransmission of data PDUs, thereby increasing the throughput performance.