The invention discloses a novel power electronic traction transformer topological structure and a control method thereof. A novel power electronic traction transformer comprises N power transformation units. Each power transformation unit comprises an H bridge converter and a middle/high frequency isolated-type DC/DC conversion unit. The N H bridge converters for an N-grade cascaded H bridge converter, and the middle/high frequency isolated-type DC/DC conversion unit comprises K DC/DC converters. Input ends of the N power transformation units are connected in series and output ends of the N power transformation units are connected in parallel. Input ends of the N-grade cascaded H bridge converter are connected in series, and output ends of the N-grade cascaded H bridge converter are disconnected. Input ends of the N DC/DC conversion units are connected with the output ends of the N-grade cascaded H bridge converter, and output ends of the N DC/DC conversion units are connected in parallel. Input ends of the K DC/DC converters are connected in series, and output ends of the K DC/DC converters are connected in series. The power balance control of the novel power electronic traction transformer comprises three parts: the direct current output voltage balance control of each H bridge converter, the output current balance control of each middle/high frequency isolated-type DC/DC conversion unit, and the input voltage balance control of each DC/DC converter of each middle/high frequency isolated-type DC/DC conversion unit.