The next generation of space-borne synthetic aperture radar (SAR) systems will emphasize on high-resolution and wide-swath imaging. For these design goals, multichannel technology in azimuth is a promising candidate and can provide global monitoring capacity for the continuous observation of a highly dynamic and rapidly changing world with high spatial resolution and short repeat intervals. In the multichannel SAR system, the nonuniform azimuth signal needs to be reconstructed when the pulse repetition frequency is different from a specific one. A reconstruction algorithm based on periodic nonuniform sampling theory has been proposed in current literature, but it is computationally rather expensive. In this paper, nonuniform fast Fourier transform is employed to reduce the computation load of the original algorithm from $O(N^2) $ to $O(N\log N) $ , where $N$ is azimuth sample number. Furthermore, a modification is implemented by taking the out-of-band energy into account to suppress the azimuth ambiguity when the signal is not band-limited, which is actually the case of the azimuth modulation of SAR with a real antenna pattern. The computation and reconstruction performances validate the proposed method’s effectiveness in multichannel signal processing and its suppression effect on azimuth ambiguity.