The invention discloses a filtering method of a sodium-potassium alloy, which comprises the following steps: (1) heating the sodium-potassium alloy to be filtered to 100-150 DEG C, keeping the temperature, and fully dissolving impurities; (2) naturally cooling a sodium-potassium alloy tank to 20-60 DEG C, settling the impurities, and further quickly transferring the sodium-potassium alloy; and (3) controlling the temperature of a filtering loop at 20-60 DEG C during the transfer process, and adopting a sodium-potassium alloy filter to further filter the conveyed sodium-potassium alloy. The invention provides the filtering method of the sodium-potassium alloy with simple operation, safety, reliability and good filtering effect.