This deep space sensor network based on DTN is an important research in modern deep space communications technologies. Bundle layer plays a key role in the network. How Bundle layer can provide services for network more rationally and efficiently is an important influencing factor to improve and enhance the network performance. This paper proposes special network architecture for this DTN-based network. Systematic study on function and structure of Bundle Protocol which runs in corresponding layer is completed. To realize this protocol, a scheme based on different functional modules is proposed. In order to solve the congestion problems in the deep-space wireless sensor networks, referencing the previous studies, this paper proposes a new congestion control algorithm which bases on persisting storing and transferring the data. Through simulation experiments, comparing to the existing congestion control algorithm, the new algorithm effectively reduces the data loss rate and the average latency in the network.