A loss measurement method on silicon-on-insulator (SOI) waveguide is proposed on the basis of Fabry-Perot (F-P) cavity theory. Through end coupling, the method utilizes the Fourier transform information of the reflection power spectrum to achieve the waveguide loss measurement. In the process of derivation, the main reason why the loss index can not be directly solved from the peak and valley values of the F-P peaks of reflection spectrum is presented. In the experiment, the loss measurement on a SOI ridge waveguide with an etching depth of 750 nm and a width of 1200 nm is achieved by using the method, which indicates that the method can be used for the loss measurement on small size low-loss waveguides with a relatively high accuracy.