A new general circulation model (GCM) which contains the region from the ground surface to the exobase has been developed and used to investigate behavior of the migrating diurnal tide for equinox during solar cycle minimum and geomagnetically quiet conditions. In particular, we study day-to-day variations of migrating diurnal tides in the mesosphere and thermosphere and their relation with migrating diurnal tides generated in the lower atmosphere. The results show that day-to-day variations of the migrating diurnal tide are evident from the upper troposphere to the thermosphere. Fluctuations of the migrating diurnal amplitude with periods of 12 and 25 days are found in the height range from 20 to 300 km, indicating dynamical coupling between the mesosphere and thermosphere and the lower atmosphere.