In this paper, a dynamic evolution control for the operation of the three-level bidirectional DC-DC converter with supercapacitor system is presented. The three-level DC-DC converter configuration is effective in reducing the stress on the power semiconductors switches and provides better performance with smaller passive components compared to two-level DC-DC converters. The proper control method is inevitable for its effective operation. The dynamic evolution control method requires only two controller parameters to be tuned for the operation of the three-level bidirectional DC-DC converter. In the dynamic evolution control method, the voltage balance control is also included in the control equation which makes its simple to design. Real-time simulation studies validate the effectiveness of the proposed control method.