Multilevel inverters with improved voltage quality are widely used in applications such as motor control and electric vehicles. The four-level active neutral point clamped (4L-ANPC) inverter effectively meets the demands for high power density and low device voltage stress. However, balancing the capacitor voltage and reducing its low-frequency voltage fluctuation are critical challenges that need to be addressed. To address these challenges, this paper proposes a “variable reference + zero-sequence injection” method that requires only three reference voltage signals to determine the injected zero-sequence components. Particularly, the expression of the midpoint current, regarding the modulation index and phase current amplitude, is theoretically derived. This reveals the fundamental connection between the zero-sequence voltage signal and the midpoint current, providing a theoretical foundation for the zero-sequence injection method in four-level inverters. Subsequently, a simulation model and an experimental platform of the 4L-ANPC inverter were developed to compare and analyze the waveforms of the upper and lower capacitor voltages, phase currents, and line voltages under different modulation methods. Additionally, the upper and lower capacitor voltage waveforms were examined for various modulation indices. The results indicate that as the modulation index increases, the low-frequency voltage fluctuation in the upper and lower capacitor voltages also rises. At a modulation index of 0.95, the “variable reference + zero-sequence injection” method effectively suppresses the fluctuation in the upper and lower capacitor voltages to be no more than 1 V. These experimental findings validate the effectiveness of the proposed method.