The invention discloses a double electrical boot electric train continuous electricity subsection passing control system and a method thereof, and relates to the technical field of rail transit three-phase power supply systems. The control system comprises variable-frequency and voltage transformation equipment, a positioning unit, and a ground operation control system; the variable-frequency andvoltage transformation equipment is used for providing three-phase power supply to an electric train; the positioning unit is mounted near the subsection position of a power supply rail; and one end of the ground operation control system is connected with the variable-frequency and voltage transformation equipment and the positioning unit respectively to collect signals, and the other end is connected with the variable-frequency voltage transformation equipment to be used for data communication. Therefore, according to the double electrical boot electric train continuous electricity subsectionpassing control system and the method thereof, the variable-frequency and voltage transformation equipment in the adjacent intervals is coordinated and controlled to supply power when the electric train passes through a subsection power supply subsection device, "no sense" subsection power supply can be realized, the load bearing efficiency and the power supply efficiency of the electric train can also be improved, the economic cost is also greatly reduced, and at the same time the favorable condition for artificial intelligence unmanned driving is also created.