This paper proposes a technique that compensates for unbalance and nonlinearity in microgrid inverters with power transformers operating in stand-alone mode. When a microgrid inverter is operating in stand-alone mode, providing high-quality power is very important. When an unbalanced, nonlinear load is connected, zero sequence current and negative sequence current occur, which leads to an unbalanced output voltage. This paper examines why the zero sequence component occurs differently depending on the structure of a three-phase transformer connected to the inverter output terminal, and it proposes a method for controlling the zero sequence component. It also uses a resonant controller to remove the harmonics that correspond to the negative sequence component and the nonlinear component. The proposed elements were verified by a Powersim (PSIM) simulation.