To study the vertical structure of temperature and humidity in the atmosphere boundary layer over the homogeneous wetland underlying surface, the twodimensional numerical model was applied to simulate the potential temperature and specific humidity profiles within 1000 m in Honghe National Nature Reserve in the summer of 2008. Besides, the numerical simulation was also used to analyse the correlation between the structure of the atmospheric boundary layer and the two main influence factors (wind velocity and roughness length), and to investigate their effects on the potential temperature and specific humidity at different heights. The results indicated that: (1) The twodimensional numerical model could provide a fair description of the vertical structure of the atmosphere boundary layer over the wetland underlying surface, the simulated results of potential temperature were superior to the results of specific humidity. (2) Wind velocity and roughness length are the main factors influencing temperature and humidity profiles over the wetland underlying surface. Wind velocity performed remarkable positive correlation with potential temperature and negative correlation with specific humidity. Wind velocity had a similar correlation coefficient with potential temperature below 60 m, and significant negative correlation with specific humidity below 200 m. The effect of wind on potential temperature and specific humidity increased with height over wetland. The effective height of roughness length on potential temperature was 60 m, and that on specific humidity was between 10 m and 20 m. Roughness length of wetland underlying surface has a significant positive correlation with potential temperature and specific humidity under the affect altitude, and its influence decreased with inerease in altitude. (3) The variation of potential temperature and specific humidity in high altitude were controlled by wind velocity mainly, but they were both influenced by wind velocity and roughness length in low altitude.