The propose of this paper is to present the systematic processes of constructing the averaged small-signal model of the three-phase grid-connected three-level neutral-point-clamped inverter with a LCL filter and to design the control system for the grid current by using the model. The systematic processes are composed of the averaging, perturbing and linearizing step about the circuit equations. In addition, this paper presents a frequency-domain analysis to design the control systems and study the system stability and the control scheme of the grid current based on the averaged small-signal model. The validity of the model is verified by the simulation and the experiments.