The method of Fabry-Perot resonant cavity （also called F-P cavity） is exploited to measure the optical transmission loss of SOI waveguides and the fiber-chip butt-coupling loss， with which three SOI waveguide channels having the same size and a length of 8.37 mm are measured. Then， the average value of SOI waveguide optical transmission loss/butt-coupling loss and the measurement accuracies are obtained， and the standard deviation of the measurements is very small. Another SOI waveguide with a length of 12.5 mm is measured using an automatic temperature control scanner and both the transmission losses and the butt-coupling losses of three repeated measurements are the same as one another， implying the stable measuring accuracies of F-P cavity method. The dual dependences of the measurement accuracy da/a of SOI waveguide transmission loss on the relative error dt_M/t_M of F-P cavity output extinction ratio and the relative error dR/R of the Fresnel reflection coefficient of SOI waveguide end-face are theoretically modelled. The simulation results show that the changes of SOI waveguide refractive index， the upper/lower cladding layers and core layer have no impacts upon the measurement accuracies of both the optical transmission loss and the fiber-chip coupling loss.The numerical simulation results are consistent with the experimental results.