Three-level simplified neutral point clamped (NPC) inverters are studied due to lower harmonics and fewer switching devices. Nevertheless, this topology needs to obtain neutral point (NP) voltage balance through either control or modulation methods. For the operation of photovoltaic application, the common-mode voltage (CMV) is needed to meet the requirements of leakage current. To address these issues, a modified predictive control method via two-layer vector selection criteria is proposed. In the first layer, the candidate switching vectors for the CMV reduction are selected. In the second layer, the P-type or N-type small vectors are selected for NP voltage balance. Then, the control method selects the optimized switching vector from the cost function consisting of the number of switching and the current, which can obtain the better performance depending on the power rating. Simulation and experimental verification results show that the modified predictive control method can reduce CMV and balance NP voltage both steady-state and transient process.