The invention discloses a composite-voltage latch-up over-current protection system and method of an arc-protection acceleration transformer. The system is composed of a setting value input circuit, a conversion decoding circuit, an arc protection signal input circuit, a processor and an output circuit. Output terminals of the setting value input circuit, the conversion decoding circuit and the arc protection signal input circuit are connected with the input terminal of the processor; the output terminal of the processor is connected with the input terminal of the output circuit; and the output terminal of the output circuit outputs a protection output quantity. Meanwhile, the invention also discloses a method of the system. Therefore, the acting time of composite-voltage latch-up current protection can be shortened; the short-circuit impact on the transformer in a fault state can be reduced; and the damages on the transformer by the short-circuit fault can be reduced.