This paper presents a practical channel estimation algorithm based on cyclic orthogonal training sequence for relay-assisted cooperative communication system. In this algorithm, the relay nodes receive the cyclic orthogonal training sequence and circularly shift them to ensure the orthogonality before retransmitting them. It is in low complexity and the destination node can be in a good condition to get the channel state information (CSI) according to the sequence. The least square (LS) and linear minimum mean square (LMMSE) channel estimators are derived and the design of optimal training sequence is given. Simulation results show that the proposed algorithm can provide a significant performance improvement in terms of robustness, accuracy and efficiency.