This paper presents a methodology for structural optimization of the power equipment composition of autonomous photovoltaic systems with storage battery replacements. Based on the fundamental principles of systemic energy research, systems theory and the theoretical framework of electrical engineering, among others, this methodology adopts a universal approach to describing climatic indicators by processing FM 12 Synop and METAR multi-year meteorological data sets.The paper gives a detailed description of the autonomous photovoltaic system, its basic elements and control algorithms. The universal storage battery model is treated separately. A comprehensive description is provided of an algorithm for calculating storage battery lifetime. The notions of partial cycle and local minimum state of battery charge are introduced. These indicators are necessary for the correct estimate of the number of battery cycles to failure. After identifying the number of cycles to failure and the average annual number of cycles, it is possible to calculate storage battery lifetime. Next, it becomes possible to consider storage battery lifetime when dealing with the structural optimization of photovoltaic power systems. Importantly, the results reveal a more than 10% increase in the LCOE indicator.Kurbulik, an autonomous energy system located in a protected area of Lake Baikal, is given as an example. The optimization results show that the combined use of renewable energy sources reduces diesel fuel consumption by 51%. Storage batteries are replaced three times every six years. The levelized cost of energy is 16.80 rubles/kW h (as compared to 34.82 rubles/kW h for diesel generation alone). The presented methodology is universal and can be applied to different locations.