Phthalate esters (phthalic acid esters or PAEs) are widely utilized during production as an inactive plasticizer, which results in serious water pollution. Ideal removal of micropollutants is difficult to achieve with traditional water treatment, but technology using nanofiltration membrane removes water micropollutants effectively owing to its unique membrane structure. To further study the rejection performance of nanofiltration membrane for PAEs, carbon nanotube-modified nanofiltration membrane was proposed to treat PAEs in water. The adsorption and rejection properties of PAEs on the surface of nanofiltration membrane were revealed by multi-factor experiments. Adsorption kinetics was also analyzed, and the adsorption isotherm of PAEs on the membrane surface was simulated. In addition, the effects of running time, molecular weight, n-octanol/water partition coefficient, and average polarizability on the performance of PAE rejection of nanofiltration membrane were discussed. Results show that the Freundlich adsorption equation simulates the adsorption of PAEs on the surface of the nanofiltration membrane, and the correlation coefficient is more than 0.998. The adsorption capacity of the nanofiltration membrane for three typical PAEs substances, namely, diethyl phthalate (DEP), dibutyl phthalate (DBP), and dioctyl phthalate (DOP), decreases in turn. At the same time, the early rejection of PAEs by nanofiltration membrane is primarily due to the adsorption of membrane surface, and the equilibrium stage depends mainly on the sieving effect of the membrane pores. This study provides a theoretical basis for the application of nanofiltration membrane in the removal of PAEs.