The invention discloses an interference cancellation and two-way cooperation channel estimation method based on affine precoding. The method comprises the steps of S1, establishing a precoding matrix and a decoding separation matrix; S2, combining information sequences and training sequences to establish data frames and carrying out precoding; S3, transmitting data signals and carrying out amplification and forwarding after data is superposed by a relay; S4, carrying out decoding separation operation, extracting training data and carrying out channel estimation on two-way parallel channels; and S5, extracting information data from target signals, carrying out symbol detection, and outputting a detection sequence. According to the method provided by the invention, the two-way relay is converted into two parallel and non-interfering one-way relay network channels; through combination of little training, the two one-way relay channels are estimated, so channel estimation is not influenced by elimination of self-interference; signal energy can be expanded to a whole band through precoding; the fading in a time-varying channel environment is overcome; and the time diversity gain is provided.