It is difficult to clarify the environmental condition in tidal flat because of the complicated interaction of atmosphere, sea water, land and creature. The thermal environment is an important factor in water quality closed relationship phytoplankton growth and activated biological. The objective of this study is to grasp the characteristic thermal from field observation and calculate the numerical thermal model simulation in the bottom mud at tidal flat. The thermal water or bottom was observed at four sites that were different in the ground level and the meteorological variables in the inter-tidal zone near Kumamoto Port. As a result, the thermal in bottom was depended on tide change and the numerical thermal model improved the accuracy with a scheme thermal diffusion.