In the amplify and forward (AF) cooperative relay communication system, the amplification of relay node's noise makes the noise of receiver no longer obey the Gaussian distribution, and hence, the traditional MMSE channel estimation algorithm is difficult to realize accurate channel estimation and the performance of cooperative relay system is reduced accordingly. This paper proposed the Linear Minimum Mean-Square Error (LMMSE) channel estimation based on delay time-domain windowing technique, and analyzed the performance of the proposed channel estimation algorithm in the frequency selective fading channel based on the wideband system. Simulation results show that the algorithm proposed can effectively suppress the impact of the noise to channel estimation result compared with traditional algorithms, and the mean square error (MSE) of channel estimation can be reduced at least an order of magnitude compared with traditional algorithms when Eb/N0 changes from 0dB to 20dB.