Mechanisms of the soil profile and aggregate stability are related to molecular level of the structure organization and the matrix properties. The soil matrix or surface of soil particles is an arena on which all interactions in soil take place. Soil matrix organizes the adsorptive layer from ions complex, adsorptive water, the organic matter and the microorganisms and immobilizated enzymes around itself. Soil matrix consists of three parts: mineral matrix (E, B horizons), organic (litter, peat) and organomineral (A horizons). The selection of the matrix into a separate part of soil particles is affected by several reasons. Soil is polydisperstive and polymineral system and its particles are not the same participation in the soil processes. The most active are clays (montmorillonite, kaolinite, hydromica) and the less active quartz and field spar among minerals. The properties of the surface layer of soil particles differ from the properties of its internal part. Matrix size is evaluated as common surface of soil (external and internal) or colloid and silt complex. This surface is heterogeneous in chemical, electrical and power properties. The active centers and clusters (group of centers with similar functions) are the most active elements on matrix which take up 1-25% of the whole matrix. Organic matrix may be in 2 forms with differences properties, which consists of organic molecules or colloid of humus. Interaction between mineral and organic matrix results to organomineral matrix and defines the processes of compartmentation in soils. The diversity of active centers and clasters on the soil surface forms the differences compartments. The active centers can be of the acid nature (hydroxyl groups, exchange cations, coordinately non-saturated cations) and basic nature (oxygen, hydroxyl groups, exchange cations), which reflect of the soil conditions and of rock composition. Also its can be of Hydrophilic and Hydrophobic and of the point (place, area) of crystal growth and new soil formation. Its form links with other matrix. The mineral matrix of all soils in Russia have acid properties: in chernozems the number of acid centers is in 3-4 greater than basic ones, in soddy-podzolic soils, the mineral matrix is represented practically only by acid centers. The feature of soil matrix is to organize matter around itself in defined order. Matrix creates adsorption layer from water, microorganisms, immobilization enzymes, ions and organic compounds. Area of the directly matrix effect is near 100 nm. The main feature of organic matrix is in the capacity to replication itself. The fresh segments of organic molecules can be built in already existing ones – process known as fragmentary exchange. The humus fragmentary exchange on the mineral matrix takes place simultaneously with the humus mineralization. As a result of its processes is the stability of the common humus content and group composition in soils with similar mineral matrix. Mineral matrix exerts the most pronounced effect on the humus formation. The 60-70% of humus is mobilized by mineral colloids. The properties of matrix humus as specific surface, density, porosity and common content are determined by the properties of mineral matrix. The matrix of clay minerals catalyzes the formation of similar to humus components. These catalytic processes do not take place without clay minerals. The initial soil mineral matrix inherited from soil formation rock creates the borders in which soil develops. So, quantity and quality of active centers on matrix define the content, features of contacts between soil particles (coagulate and phase) and degree of its interaction. Matrix interactions result to aggregate formation. The mechanical strength of soil aggregates is directly proportional to size of the soil matrix. Aggregate structure forms all physical properties of horizon and profile. Thus, the concept of matrix organization of soil allows us to observe the effect of properties of atoms, ions and molecules on formation of more organized elements of the soil structure. The developing of mineral matrix to organomineral and the increase of its sizes are in soil formation. The initial mineral matrix forms the organomineral, the contacting interactions with other matrix and compounds and organizes matter around itself in some order. Mineral matrix determines the borders in which soil develops. It keeps the processes of soil formation after its degradation as fires and humus mineralization. The aggregate stability and stability of the soil profile are determined by the matrix organization. Matrix organization is the main mechanism in the stability of soils as biosphere systems. It is dynamic (change, interaction with solution) and creates the conditions for dynamic of soil properties.