The invention relates to method and equipment system for separating and recovering organic oxygen-containing compounds in a Fischer-Tropsch synthesis water phase. The equipment system is integrated by adopting twelve towers including a mixed acid cutting tower, an acetaldehyde rectifying tower, a methanol/ethanol dividing tower, a methanol extraction rectifying tower, a methanol rectifying tower, an acetaldehyde removing tower, an ethanol tower, a propanol concentration extracting tower, a propanol intermittent azeotropic distillation tower, a carboxylic acid extraction tower, a carboxylic acid intermittent rectifying tower and an extraction agent recovering tower matched with the carboxylic acid extraction tower for use. By applying the method and equipment system disclosed by the invention, more than ten kinds of organic oxygen-containing compounds such as acetaldehyde, acetone, methanol, ethanol, normal propyl alcohol, normal butanol, acetic acid, metacetonic acid, butyric acid, butanone and the like can be separated from raw materials; and the products can respectively reach the industrial purity. The method and equipment provided by the invention are economic, effective and reasonable; and according to the method and equipment, efficiency of Fischer-Tropsch synthesis industrial enterprises can be greatly increased, production cost is reduced and goal of clean production can be achieved.