The invention discloses a marsh gas purifying system and a purifying method thereof. The marsh gas purifying system comprises a gas-water separator and a plurality of desulfurizing towers. The marsh gas purifying system is characterized in that the multiple desulfurizing towers are arranged in parallel, the gas inlet of the gas-water separator is connected with a marsh gas fermentation device through a main marsh gas pipe, one end of the desulfurizing towers which are arranged in parallel is connected with the gas outlet of the gas-water separator through the marsh gas main pipe, and the other end of the desulfurizing towers is connected with a gas storage device through the marsh gas main pipe. By means of the marsh gas purifying system, people can supplement water to a positive and negative pressure protector easily, pressure in a marsh gas fermentation tank keeps constant, fracture of the marsh gas fermentation tank is prevented, and dewatering is carried out firstly through the gas-water separator, which facilitates marsh gas desulfurizing; the desulfurizing towers are connected in parallel, online desulfurizing agent replacing can be carried out by adjusting different valves.