Infrared small target detection is one of the key techniques in infrared search and track system, and the essence of infrared small detection is background suppression and target enhancement. Inspired by that fact that phase spectrum is proved to be more effective to extract the salient areas than the amplitude spectrum of Fourier transform, a new infrared small target detection method based on phase spectrum of quaternion Fourier transform (PQFT) is proposed in this paper. First of all, four features including intensity, motion, gradients of horizontal and vertical directions are used to construct a quaternion of PQFT. Then, the target enhancement map that highlights the salient regions in the time domain is computed using the inverse PQFT. At last, the real target is directly segmented by an adaptive threshold. Both qualitative and quantitative experiments implemented on real infrared sequences evaluate the proposed method, and the results demonstrate that our method possesses more robustness and effectiveness in terms of background suppression and target enhancement when compared with other conventional methods.