The main mechanism of interaction between lower neutral atmosphere and ionosphere are the upward propagating atmospheric planetary waves. In the Institute of Solar-Terrestrial Physics RAS the experimental investigations of the interaction between different atmospheric layers from the stratosphere up to ionospheric E- and F-regions were carried out. The long-term database of some midlatitude upper atmosphere parameters was used (the horizontal thermosphere/ionosphere wind, the minimal vertically reflected from the ionosphere radio-frequency fmin, total ozone content, stratospheric temperature). The seasonal variations and significant non-zonality (longitudinal dependence) of the quasi-periodical structure were revealed. The influence of solar and geomagnetic activity periodicities from above and stratospheric thermo-baric field from below on the upper atmosphere processes are evaluated. In spite of significant changeability of planetary waves in the atmosphere- ionosphere system (from day to day, seasonal, from year to year, with solar cycle etc.) there are some similarities for the different atmospheric layers. The empirical model for the lower thermosphere wind field quasi-periodical structure was constructed. It is shown that increasing of planetary waves (wave-numbers 1 and 2) activity leads to the decreasing of the prevailing zonal wind velocity. We consider the atmosphere- ionosphere planetary waves as indicators of the complex disturbances in the Sun-Earth system and important element of upper atmosphere climate.