The invention discloses a heat-assisted variable-section roll forming machine system and a method thereof. According to the system, a variable-section roll forming system comprises an uncoiler, a straightening machine, a feeding machine, a variable-section roll forming unit and a flying shear machine sequentially according to the machining sequence of plates, an electromagnetic auxiliary heating system comprises a high-frequency furnace and a temperature sensor, a computer control system comprises a variable-section roll forming control system and the electromagnetic auxiliary heating system, the uncoiler, the straightening machine, the feeding machine, the variable-section roll forming unit and the flying shear machine are connected with the variable-section roll forming control system, the high-frequency furnace and the temperature sensor are connected with the electromagnetic auxiliary heating system, and the variable-section roll forming control system is in communication connection with the electromagnetic auxiliary heating system. By the aid of the system and the method, the work hardening phenomena of plates made of magnesium alloys, aluminum alloys and high-strength steels can be reduced, the forming limit of plates can be improved, the deformation resistance can be reduced, the uniformity, the toughness and the malleability of material flowing can be improved, and the forming performance of plates can be improved.