This invention relates to a method for super-deep removing aromatics in two steps from natural gas synthetic oil, in which, a natural gas synthetic oil raw material and H enter into a first fixed bed reactor at the same time to contact and react with a hydrofining catalyst, the reacted substance from the first reactor enters into a second fixed bed reactor directly to contact and react with an aromatic saturated catalyst to get a gas-oil mixture to be separated and fractionated to get the target product, the gas with rich H is used circularly by a circulating compressor.