The three-dimensional new corrdinate system over a single hill double hills and complex terrain with a single hill and a rectangular obstacle was generated using a body-fitted coordinate system. Control of the coordinate line distribution in the field was executed by generalizing the elliptic generating system to Poisson equation. ▽2ξ=P. The new coordinate system was well fitted to the surface boundary of single hill and double hills. But in the case of complex terrain with hill and rectangular obstacle there was smoothing tendency around the rectangular obstacle. In order to show the validity of the body-fitted coordinate system the heat diffusion equation was transformed and the temperature distribution was calculated over the various terrain. The results showed the temperature distribution was very symmetrical and stable around hills and obstacle. As a result the couple of a body-fitted coordinate system and the heat diffusion equation were executed successfully. Wind field over complex terrain with hill and rectangular obstacle which represent urban area was simulated stably in body-fitted coordinate system. The qualitative result show the enhancement of wind speed at the upwind direction of a hill and a rectangular obstacle and the recirculation zone at the downwind direction.