Hydrophobicity of natural organic matter (NOM) is one of its fundamental properties that influence the environmental fate of pollutants and the performance of many water treatment unit processes. In this study, a high-throughput method was developed for NOM hydrophobicity measurement based on the phase separation technique in the 96-well format. It measures the partition coefficients of NOM (KATPS,IL) in an ionic liquid (IL)-based aqueous two-phase system (ATPS). The ATPS was made of 1-butyl-3-methylimidazole bromide solution and a salt solution containing potassium phosphate monobasic and potassium phosphate dibasic. The partition of NOM in IL-based ATPS is mainly affected by its hydrophobicity. log KATPS,IL linearly correlated with the commonly used NOM hydrophobicity scales, including (O + N)/C, O/C, and aromatic carbons. KATPS,IL provided a more accurate assessment of NOM hydrophobicity than spectroscopic indices. Furthermore, KATPS,IL can predict the organic carbon–water partition coefficients for hydrophobic organic chemical sorption to NOM based on the two-phase system model. The high-throughput KATPS,IL measurement and the two-phase system model can be applied to real surface water samples. Our results suggest that the proposed high-throughput method has great potential to be applied to monitor NOM hydrophobicity for environmental risk assessment and water treatment purposes.