Provided is a device for producing ultra-low sulfur biodiesel. The device for producing ultra-low sulfur biodiesel is a two-stage processing device, comprising a two-stage purification unit, a two-stage enzyme reaction unit, a two-stage distillation unit, and a decompression rectification unit. The present invention is green and environment-friendly, effectively and completely removing sulfur-containing impurities from the raw material, eliminating the attack of a sulfur-containing group in the synthesis process on fatty acids, and providing sufficient conditions for obtaining ultra-low sulfur content methyl esters in the product section.