The invention discloses a network coding-based transmission method of two-way relay multi-user complex pairing. A relay is used for distributing identical spread spectrum codes to each pair of communication users on both sides and carrying out network coding on received information; time slots of communication for both parties are reduced and system throughput is added; at the same time, the relay is used for carrying out networking coding on the received information, so that conditions for interference suppression of the communication process are created; and thus, multi-user interference caused by poor cross correlation of the spread spectrum codes is reduced. In the communication process of the method, only two time slots are needed for an uplink and a downlink. According to the methodprovided by the invention, multiple defects in a traditional CDMA (Code Division Multiple Access) system are solved: in a complex pairing relationship, a sender pairing communication can be finished by repeated spread spectrum of a sender; when many users exist, the system generates serious multi-user interference; and the network throughput is low. According to the invention, networking coding is used; superposed information bits are obtained during de-spreading so as to provide a basis for interference suppression; and multi-user interference, which cannot be suppressed by the traditional CDMA system, caused by complex pairing is solved.