Abstract: An urban canopy model is incorporated into the Nanjing University Regional Boundary Layer Model. The simulation results of urban temperature with the urban canopy model are better than those with the traditional slab model, and are in more reasonable agreement with the observations, especially in the night time. The incorporated model is used to study the effect of buildings morphology on urban boundary layer and meteorological environment by changing urban area, building height and building density. By analyzing the results of sensitive experiments, the results are as followings: (1) When the urban area is expanded, the urban boundary layer heat flux increases, the thermal turbulence strengthens, the turbulent momentum flux and kinetic energy increases, and the surface air temperature also increases. The stability of urban atmospheric stratification is affected to different extents at different times in a day. (2) When the building height increases, the aerodynamic roughness height and zero plane displacement height of urban area increase, and the ratio of building height to street width also increases. Therefore, the increase in building height results in decreases in the surface heat flux, and decreases in urban surface temperature, mean wind speed and turbulent kinetic energy in the day time. While at night, as the more heat storage released by higher buildings, the thermal turbulence is more active and the surface heat flux increases, so urban temperature is higher. (3) As the increase in building density, the aerodynamic roughness height of urban area decreases, and the effect of urban canopy on radiation strengthens. The increase in buildings density results in decreases in urban surface heat flux, momentum flux, and air temperature, the increase in mean wind speed, and the weakening of turbulences in the daytime. While at night, urban temperature increases due to the release of more heat storage.