The invention discloses a deep space multi-file transmission method based on fountain codes. According to the method, the codeless characteristic of the fountain codes is fully utilized, and a forward channel is fully utilized to reduce the data size on a backward channel, so that the link utilization rate is increased, and time delay is shortened. According to latest packet loss rate information, required coding redundancy is calculated, the success rate of primary transmission is increased, and the redundancy is effectively controlled; with respect to the receiving party, a united decoding algorithm is adopted, coded information is fully utilized, the calculation complexity is lowered, and the success rate of decoding is increased; in the retransmission process, different protection strategies are adopted according to different packet loss conditions to reduce retransmission frequency; a multi-file united transmission strategy is adopted, feedback information of the receiving party is not waited for, files to be transmitted are processed directly, link resources are fully utilized, and time delay is shortened; on the basis of a CFDP, a coding packet is sent as content of a data field, so that good compatibility and practicability are guaranteed. By means of the deep space multi-file transmission method based on the fountain codes, the problems of huge transmission delay, link time varying and channel asymmetry are solved in a targeted mode, the redundancy is effectively controlled, the transmission frequency is reduced, and the goal of efficient and reliable transmission of deep space files is basically achieved.