The invention relates to a processing method for two-step dewaxing of Fischer-Tropsch synthesis oil. The method comprises the following steps of (a) stably hydrogenating for saturating olefin in the Fischer-Tropsch synthesis oil, thus obtaining first effluence, feeding the first effluence into a first gas-liquid separator to obtain a first gas phase and a first liquid phase, feeding the first liquid phase into a distilling device A, distilling to obtain light fuel fraction, high-boiling-point wax and wax-containing lubricating oil fraction; (b) sequentially carrying out isomerization dewaxing and post-refining saturation on the wax-containing lubricating oil fraction, converting wax with a relatively low boiling point in the wax-containing lubricating oil fraction into isoparaffin in an isomerization dewaxing reactor, re-entering a post-refining reactor for stably saturating, thus obtaining second effluence, feeding the second effluence into a second gas-liquid separator to obtain a second gas phase and a second liquid phase, feeding the second liquid phase into a distilling device B, and thus obtaining light fuel fraction and lubricating oil base oil through distilling. Not only is the problem that flocculates are produced during a hydroisomerizing process solved, but also the follow-up operating load is reduced, and the cost is reduced.