The paper presents mathematical models of solar energy fluxes considering cloud cover, data model from the experimental unit, and energy balance model. Also, the method of data rectification due to experimental measurements is described. It proposes the configuration of a digital twin of an isolated hybrid energy system that includes three channels: simulation (theoretical), hardware (physical) and secondary. Preliminary results of isolated hybrid energy system functioning are analysed. The developed system allows qualitative and quantitative analyses of energy flows, which contributes to more efficient management of energy resources and improved reliability of energy supply, in particular by detecting critical time periods with energy shortages.