An adaptive windowed Fourier transform (WFT) profilometry based on the ridge algorithm of S-transform is presented. The practical use of one-dimensional S-transform in processing fringe pattern is discussed, and the S-transform expression is derived. Every point′s instantaneous frequency is calculated by taking advantages of S-transform′s frequency sensitivity and its ridge idea. The influence of φ″(b) on the ridge of S-transform is derived in the sharp phase transition region, and a more accuracy instantaneous frequency is calculated after removing this deviation. Then an accurate phase map of fringe pattern is calculated by using the windowed Fourier transform based on the window which is the reciprocal of instantaneous frequency. Finally, the simulation which compares the accuracy of phase map calculated by WFT based on S-transform (SWFT) before and after removing the influence from deviation of φ″(b) is carried out. Experiments show its advantages in anti-noise and accuracy of the wrapped phase comparing to WFT based on wavelet-transform (WWFT).