The invention relates to a method for treating oxygen-containing organic matters in Fischer-Tropsch synthesis reaction water. According to the method, Fischer-Tropsch synthesis reaction water is subjected to following treatment steps: (a) primary separation, concentration and separation, (b) carbonyl compound hydrogenation, (c) carbonyl compound cutting, (d) mixed alcohol dehydration, (e) solventrecovery, (f) ethanol separation, (g) methanol removal and separation, (h) isopropanol separation, (i) propanol cutting, (j) n-propanol separation, and (k) 2-butanol separation to obtain basic organicchemicals such as ethanol, isopropanol, n-propanol, 2-butanol and a mixed alcohol. Compared with the prior art, the method has the advantages that the concentrated Fischer-Tropsch synthesis water rich in alcohols, aldehydes, ketones, acids, and esters is directly hydrogenated into a mixed alcohol water solution, the separation technological process is simple, and the product purity is high.