X-ray pulsar navigation is a promising technology for autonomous spacecraft navigation. The key measurement of pulsar navigation is the time delay (phase delay). There are various methods to estimate phase delay, but most of them have high computational complexities. In this paper, a new method for phase delay estimation is proposed, which is based on the time-shift property of Discrete Fourier Transformation (DFT). With this method, the time complexity can be greatly reduced. Also, a delta-function approximation can be used to further decrease the computational cost. Numerical simulation shows that the proposed method is effective for phase delay estimation, and the reduced complexity makes our method more suitable for on board implementation.