The invention relates to an ETC and MTC mixed lane charging system and a control method thereof. The charging system comprises an ETC system and an MTC system, the ETC system comprises an ETC industrial personal computer, and a first ground induction coil, a second ground induction coil, and a microwave antenna electrically connected with the ETC industrial personal computer, the MTC system comprises a charging booth, an MTC controller electrically connected with the ETC industrial personal computer, a first automatic rail connected with a port of the MTC controller, a first rail-falling coil matched with the first automatic rail in an induction manner, and an induction coil, the first ground induction coil, the second ground induction coil, the microwave antenna, the induction coil, the charging booth, and the first automatic rail are arranged on a lane in sequence, the induction coil and the first rail-falling coil are both connected with the ETC industrial personal computer via single lines, and the first automatic rail is electrically connected with the ETC industrial personal computer. According to the charging system, the ETC system and the MTC system are mixed on the same lane, vehicles with OBUs or without OBUs can both pass, the resource idling of the ETC lanes is avoided, the utilization rate of the lanes is increased, and the passing of the vehicles is facilitated.