To solve the problem of midpoint potential balance in a three-level photovoltaic inverter during fault ride-through, this paper proposes a novel deep carrier overlapping PWM (DCO-PWM) method based on existing pulse-width modulation and midpoint potential balance methods. This method increases the overlap depth of upper and lower carriers, thereby weakening the influence of the middle vector on the midpoint potential and achieving controllable midpoint potential balance and grid-connected current in fault impact and high reactive current conditions. Because of the increase in the switching frequency of power devices by DCO-PWM, a modulation strategy based phase switching method is developed. Only when the midpoint potential difference exceeds the set threshold is the intermediate phase of the modulation wave switched to DCO-PWM, while the conventional carrier phase disposition PWM (CPD-PWM) is still used for other states, thereby reducing the harmonic content of grid-connected current and device switching losses. Experiments have verified that the above method can effectively enhance the control of grid-connected current and midpoint voltage during the low-voltage fault ride-through of a three-level inverter, thereby ensuring the safe and reliable ride-through of the fault state.