The article substantiates the necessity of organizing the control system of modern lithium-ion batteries. Passive and active methods of cell balancing are described. The method of increase of efficiency of modes of accumulation of electric energy by means of the special electronic control device (the intellectual controller) and its further use for power supply of the functional equipment is considered. The structure of the intelligent controller as a part of the autonomous power supply system with the description of its main functional units and purpose is presented. Practical results of application in the intellectual controller of original adaptive control algorithms defining modes of operation of lithium-ion drives depending on various environmental conditions are resulted. The results of the analysis obtained by the results of experimental operation of the battery system, reflecting the qualitative and quantitative advantages of the proposed method.