The optical loss caused by Waveguide Sidewall Roughness （SWR） of Silicon-on-insulator （SOI） is one of the restrictions to the adoptions of silicon photonic integrated circuits. In this paper， the anisotropic SWR of an SOI waveguide is measured by Conformal Laser Scanning Microscope （CLSM） and with introduction of a Three-dimensional （3D） anisotropic SWR， the traditional theoretical model for defining the Optical Propagation Loss （OPL） coefficient， so that a more accurate theoretical model is obtained. Numerical simulations show that the waveguide structure determined Correlation Length （CL） and the SWR have the synchronous effects on the OPL. Fabry-Perot （F-P） cavity modulation resonance output is used to accurately measure the OPL， and the measured values are agreeable with the simulation result， implying the improved model has more believability. For a waveguide with a 4 μm width， when the average horizontal and vertical SWR values are 22 nm and 23 nm， respectively， the simulation results of OPL coefficient for both TE- and TM-mode are 4.5~5.0 dB/cm， while the experimental result is 4.9 dB/cm. Hence， the outcomes and conclusion obtained are very valuable to be referred for research and development of SOI waveguide devices.