The invention belongs to the technical field of wireless communication, and discloses a channel estimation method of a full-duplex relay system based on a Chu sequence. The method comprises: using a non-blind estimation algorithm, using a Chu sequence and an OFDM symbol as sending data, after channel transmission, the received Chu sequence and the Chu sequence of a sending end being subjected to cross-correlation at a receiving end, and a cross-correlation value obtained by the received Chu sequence and the Chu sequence of the sending end being an impulse response estimation value of a channel; carrying out convolution on the estimated channel value and the Chu sequence of the sending end to obtain a value which is a reconstructed signal; and subtracting the received signal from the reconstructed signal, and performing self-interference elimination. The method starts from two aspects of theoretical simulation and USRP practical simulation, uses the Chu sequence as a training sequence to estimate the same-time same-frequency full duplex relay loop channel, generates a reconstructed signal according to the estimated self-interference channel information, and achieves the offset of the self-interference signal. The transmitting end and the receiving end perform transmission by using two USRPs, and the relay equipment performs simulation by using an amplification forwarding protocol.