In this paper the methodology of the Causal Oriented Graph (COG) is used for the modelling of a flying capacitor cell chopper. The issues of this study is a best understanding of the operating of this particular converter in order to obtain a more precise design of the control system. The obtained modelling shows that high-voltage multi levels are obtained by combination of two different three-level functions (conversion functions). Therefore a novel PWM strategy is deduced. It consists of separating the modulation period for creating two fictive modulated voltage systems via the direct width modulation and the position setting of both conversion functions. The redundancy of the different switches configurations for the voltage half value allows to use a particular modulation technique which limits the deviations of the half-value voltage. Switching patterns are deduced and a decoupling control of the capacitor voltage and the supply current is designed.