In order to solve the networking communication problem of the main-subsidiary satellite cluster under discrete and sparse topology and to ensure the demand of real-time interactive remote control telemetry and task information between satellites, this paper proposes a set of communication system architecture and inter-satellite networking protocol stack design scheme according to the hierarchical and clustered spatial topology characteristics. Firstly, in the design of the network layer, the data structure of the network layer, the subnet cluster head selection backup mechanism based on the multi-weight priority cost function and the process of the sub-satellite network access are given respectively. Secondly, in the data link layer, the data is processed hierarchically according to the subcontracted remote control and subcontracted telemetry system. Then, in the design of the physical layer, the spread frequency hopping is used as the communication system of the inter-satellite link, and the time division multiple access method is used to realize the multi-user communication of the satellite cluster, and the specific communication index of the inter-satellite link is given. Finally, the link calculation of inter-satellite communication is carried out. The calculation results show that the physical layer design meets the communication requirements of each satellite.