In this study, a robust control method of a serial multicellular inverter is suggested. This particular hybrid system represents a combination of three switching cells interconnected via two flying capacitors. These continuous and discrete variables confer a hybrid dynamical behavior which induces difficult control problems. To tackle these problems, a comparison between two different approaches has been done. First, we propose the conventional PWM control with triangular carriers. Then, a new control concept based on Petri Nets was developed and tested. This methodology shows the versatility of controlling the flying capacitor voltages and the output current. Provided simulation results certify the efficiency and the robustness of Petri Nets formalism to control this type of converters.