The invention relates to an SDS-PAGE rapid decoloring method and a special decoloring cup thereof. The method comprises the following steps: (1) gel cleaning: after electrophoresis gel dyeing is ended, cleaning the gel for 2-3 times with deionized water and the like; (2) pre-decoloring: putting the gel in the decoloring cup holding water, heating to the temperature about 80 DEG C and then discharging the water in the decoloring cup, and moreover, repeating the process for 2 times; and (3) decoloring: adding enough water to the decoloring cup; heating to the temperature which is 80 DEG C and then changing the water; then heating; recycling in such a way until the background is clean and strips are clear to finish the decoloring. The invention has the advantages that: 1. the deionized waterand the like is used as a decoloring solution instead of a methanol-glacial acetic acid solution, and therefore, the cost is low and environmental pollutions can not be generated; 2. the whole decoloring process is finished by matching with a special decoloring device and utilizing a heating method in 30-40 min, i.e. the method is convenient and rapid and accelerates test progress; 3. the method has simple operation and can very conveniently conduct a decoloring test without preparing a special decoloring solution by only utilizing the existing heating equipment of a laboratory and adopting the special decoloring device.