Three-level PWM rectifiers applied in medium voltage applications usually operate at low switching frequency to keep the dynamic losses under permitted level. However, low switching frequency brings a heavy cross-coupling between the current components $i_d$ and $i_q$ with a poor dynamic system performance and a harmonic distortion in the grid-connecting current. To overcome these problems, a mathematical model based on complex variables of the three-level voltage source PWM rectifier is firstly established, and the reasons of above issues resulted from low switching frequency have been analyzed using modern control theory. Then, a novel control strategy suitable for the current decoupling control based on the complex variables for $i_d$ and $i_q$ is designed here. The comparisons between this kind of control strategy and the normal PI method have been carried out. MATLAB and experimental results are given in detail.