Network coding, as a new technique to improve the throughput, is studied combined with multi-relay model in this paper to address the challenges of long distance and power limit in deep space communication. First, an amplify-and-forward relaying approach based on analog network coding (AFNC) is proposed in multi-relay network to improve the capacity for deep space communication system, where multiple relays are introduced to overcome the long distance link loss. The design of amplification coefficients is mathematically formulated as the optimization problem of maximizing SNR under sum-power constraint over relays. Then for a dual-hop relay network with a single source, the optimal amplification coefficients are derived when the multiple relays introduce non-coherent noise. Through theoretic analysis and simulation, it is shown that our approach can achieve the maximum transmission rate and perform better over single link transmission for deep space communication.