Because of the high complexity and large scale of LTE-A multi point cooperation, it is difficult to eliminate the multi point cooperative asynchronous interference directly when the asynchronous interference is counteracted. A LTE-A multi-point cooperative asynchronous interference cancellation method based on sparse Fourier transform is proposed. Through the analysis of LTE-A heterogeneous network environment and interference situation. Fourier transform method is introduced to sparse the LTE-A signal so that it can achieve sparse feature conditions and describe the signal in sparse representation. According to the signal by coordinated multi-point asynchronous interference in LTE-A, part of the large sparse coefficient as the valid signal, sparse coefficients smaller as part of coordinated multi-point asynchronous interference, based on sparse feature interference in sparse signal based on the separating part and the interference part, so as to realize the coordinated multi-point asynchronous interference cancellation. The experimental results show that the improved method can effectively counteract LTE-A coordinated multi-point asynchronous interference, the power spectrum of the output offset and SINR values closer to the power spectrum of the output without interference and SINR value, and guarantee the network service quality, has a certain practicality..