This paper examines the problem of synthesizing a two-loop control system for a three-phase voltage source inverter designed for an autonomous power supply system. This type of DC/AC converters is an essential part of power supply systems with renewable energy sources as primary sources, and, accordingly, must corresponds to the requirements for the electric power quality. These requirements are met through circuit design solutions, as well as through the construction of high-precision automatic control systems. The system integrates: a hydrogen electrolyzer, a hydrogen storage system, and a hydrogen fuel cell. The paper proposes a method for calculating the parameters of PI controllers with resonant components, based on the time-scale separation method and allowing independent adjustment of the controller components. The introduction of a resonant component ensures high tracking accuracy for a desired main voltage harmonic and selective suppression of external harmonic influences. The proposed approach allows to synthesize an automatic control system that significantly improves the quality of the voltage inverter output parameters.