The voltage balancing of neutral point and two flying capacitors is a great challenge in five-level Buck/Boost converter. Based on the principle of phase shift control and the capacitor voltage regulation, the influence of the neutral point voltage regulation on the flying capacitor voltage is first analyzed. Then, a synchronous phase shifting decoupling control method is proposed, which makes the capacitor voltage regulation almost independent of the neutral point voltage and eliminates the coupling of the system. Based on this, the quantitative relationship between phase shift ratio and the increase of neutral point voltage and flying capacitor voltage is derived. This method makes the voltage balance system immune to the inductor current and carrier waveform, the output voltage is not affected by the capacitor voltage regulation, which is conducive to the design and analysis of the controller. The experimental results based on the 1.5 kW prototype verify the analysis results and the excellent voltage balance performance.