The obtaining of quantitative characteristics of environmental influence on vegetation vital activity and valuation the feedback effects of canopy influence on turbulence and meteorological regime in the atmospheric boundary layer over it are the two principal purposes of the modern researches of energy and matter exchange in natural vegetation canopies and crops. The information taken from the experimental study of this system allows to obtain mainly the segmental information about some attributes of the complex multifactor process of the canopy-environment interaction. The solution of the problem concerning the environmental changes impact on natural vegetation ecosystems and crops can not likely be achieved with using the field or laboratory experiments only. An essential role in the solution of the problem like this should play the mathematical modeling because using this method of investigation we are able to joint in multi-combined models our modern knowledge about many concrete processes determining the complex energy and matter interaction between inhomogeneous vegetation and its environment. There are many problems which could be successfully studied by the model methods. Besides others they include the problem of anthropogenic climate and environment changes impacts on natural vegetation and crops productivity. In the paper which will be submitted the detailed universal model for energy and matter exchange in horizontally inhomogeneous forest canopy and in atmospheric boundary layer over it is presented. The processes descried on the model are solar radiation penetration, wind and turbulence, heat and water transport, biomass temperature regime, and carbon dioxide assimilation. The model developed has been tested in many computer numerical experiments in the context of one, two and three-dimensional non-stationary atmospheric environment as well as to the natural concrete conditions of two forest areas.