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Nowadays, an intensive development of multilevel inverters has been seen in hybrid and fuel cell electric vehicles. For this, a high voltage cascade inverter with step pulse PWM strategy is an applicable topology as it can reduce electromagnetic interference as well as switching losses on power devices. The converter is usually controlled with a look-up table of commutation angles, which are computed off-line base on an assumption of equal dc voltage sources. However, in reality, the inequality of these dc voltage sources can occur due to different charging/discharging processes and this reduces the quality of output voltages such as the existence of low order harmonics and an error in fundamental voltage. To overcome this problem, PWM angles in the look-up table can be changed according to different cases of dc source variation. However, this solution may require a large memory for the look-up table. Thus, off-line PWM strategy in case of dc voltage source variation may not be a suitable approach to control the converter. In this paper, an on-line step pulse PWM method will be proposed to control fundamental voltage and reduce the amplitudes of low-order harmonics to possibly low values. Similar to the original on-line method, the control principle between two defined trajectories will be appropriately modified for solving the problem. The principle is mathematically formulated, and demonstrated by simulation results.