This study examined the effectiveness for degradation of hydrophobic (HPO), transphilic (TPI) and hydrophilic (HPI) fractions of natural organic matter (NOM) during UV/H2O2, UV/TiO2 and UV/K2S2O8 (UV/PS) advanced oxidation processes (AOPs). The changing characteristics of NOM were evaluated by dissolved organic carbon (DOC), the specific UV absorbance (SUVA), trihalomethanes formation potential (THMFP), organic halogen adsorbable on activated carbon formation potential (AOXFP) and parallel factor analysis of excitation–emission matrices (PARAFAC-EEMs). In the three UV-based AOPs, HPI fraction with low molecular weight and aromaticity was more likely to degradate than HPO and TPI, and the removal efficiency of SUVA for HPO was much higher than TPI and HPI fraction. In terms of the specific THMFP of HPO, TPI and HPI, a reduction was achieved in the UV/H2O2 process, and the higest removal rate even reached to 83%. UV/TiO2 and UV/PS processes can only decrease the specific THMFP of HPI. The specific AOXFP of HPO, TPI and HPI fractions were all able to be degraded by the three UV-based AOPs, and HPO content is more susceptible to decompose than TPI and HPI content. UV/H2O2 was found to be the most effective treatment for the removal of THMFP and AOXFP under given conditions. C1 (microbial or marine derived humic-like substances), C2 (terrestrially derived humic-like substances) and C3 (tryptophan-like proteins) fluorescent components of HPO fraction were fairly labile across the UV-based AOPs treatment. C3 of each fraction of NOM was the most resistant to degrade upon the UV-based AOPs. Results from this study may provide the prediction about the consequence of UV-based AOPs for the degradation of different fractions of NOM with varied characteristics.