Abstract: A high resolution and nonhydrostatic WRF (weather research and forecasting) mo del were used to study the intensity and structure changes of super Typhoon Saom ei (2006). Firstly, the effect on the intensity and structure changes of Typhoon Saomei (2006) by adopting the parameterization scheme of roughness length of Makin. The result shows that the intensity change tendency of the simulated TC is more agreed with the intensity variation of the best track data than that of con trol experiment, when the new scheme is applied. It also indicates that the inte nsity prediction of Typhoon Saomei (2006) has been improved, but there is no any effect on its forecasting of track. The simulated TC structure is more coincide d with the real structure of Typhoon Saomei (2006) by verifying the nonconvent ional data from QuikScat, TRMM, and radar data, with reproducing its “Double ey ewall" and “Annular" structure in the inner core region. Secondly, the final in tensity of the model storm is significantly increased by using of the new parame terization for Typhoon Saomei (2006) boundary layer processes, compared with the traditional extrapolation, while the physical factors in its boundary layer hav e dramatically changes above 40 m/s, in particular, during the period o f the strongest intensity of TC, the averaged tangential, radial, and vertical wind, temperature anormaly, eddy kinetic energy, and absolute angular momentum i n its inner core region are increasing with the decrease of the sea surface drag coefficient, C d, in TC eyewall. Distributions of all the physical element s around 20-40 km of in the eyewall regions of Typhoon Saomei (2006) affect on i ts intensity and structure changes. Furthermore, the possible effect of large sc ale environmental vertical wind shear and SST in model on Typhoon Saomei (2006) intensity and structure changes was finally analyzed. And the negative effect of large scale environmental vertical wind shear on the TC intensity changes is is sued when Typhoon Saomei (2006) suffering intensification and weakening.