S transform is a time-frequency analysis technique which combines the advantages of both short-time Fourier transform and wavelet transform. It maps a one-dimensional spatial signal into two-dimensional time-frequency domain and has a perfect time-frequency resolution. S transform has direct relation with Fourier transform and wavelet transform, and has the similar multiresolution ability of wavelet transform. It can be derived from Fourier transform coefficient and wavelet transform coefficient of a signal respectively, but the key technology that the implementation of S transform by wavelet analysis algorithm applied in three-dimensional optical measurements is rarely related at present. Focusing on the implementation of S transform by wavelet analysis algorithm, the application of S transform in three-dimensional optical measurement based on structured light projection is disussed, especially the selection of the frequency factor in S transform for obtaining good reconstruction. The reconstructed results of S transform profilometry based on fast Fourier transform and that based on wavelet transform are compared. The computer simulations and experiments verify our analysis.