During the production of UO2 kernel for the high temperature gas-cooled nuclear reactor, a large amount of low-level radioactive organic wastewater (LLROW) containing ammonia, uranium and organic compounds are generated. The current treatment process is suffered from the production of radioactive solid wastes, low adsorption efficiency of organic matters and the frequent membrane fouling during RO process. In this study, vacuum membrane distillation (VMD)-Fenton oxidation process was developed for the deep purification of the LLROW. The process parameters were optimized and the system performance was evaluated. As a result, all major contaminates such as uranium, NH3-N, TN and COD could meet the GB8978-1996 (secondary standard) and GB/T31962-2015 (B standard) for direct discharge. The membrane fouling was also studied by membrane autopsy as well as the quantum calculation. It was found that weak hydrogen bonds were formed between PTFE membrane and contaminants while the membrane fouling could be recovered by 0.1 M HCl cleaning.