This article presents the discussion and comparison of two solar controller operation algorithms. According to these algorithms, the solar controller can operate in maximum power point tracking mode and battery charging mode, which is characterized by the maintaining an optimal charging current with the limiting of battery voltage. The paper presents the block diagrams of the maximum power point tracking mode algorithm and battery charging algorithm. The study of processes in an autonomous power supply system using the physical layout and simulation model, showed the correctness of the proposed algorithms. A quantitative comparison of the efficiency of the power supply system was made using the constant and variable step maximum power point tracking algorithms.