Rare information is available on fouling behavior of customized nanofiltration (NF) membrane evoked by pharmaceutically active compounds (PhACs) under real multiple influent matrices pretreated by ultrafiltration module beforehand. To this end, a novel tight NF membrane with excellent perm-selectivity and antiadhesion was fabricated and used to assess its separation performance/mechanism and fouling behavior to a broad range of small molecular PhACs in the context. The adsorption ratio results revealed that the affinities between five selected PhACs and the customized nanocomposite membrane surface were all much weaker (below 5.5%) than the solute-solute interacting forces (between 23.6 and 83.2%), whether for natural or synthetic complex micropollutants. The predominant membrane fouling could be interpreted by the incomplete blocking model in the permeation of both influent conditions. For neat nanocomposite membrane, the order of critical factors important on separation mechanism was electrostatic effect, adsorption and steric hindrance. The fouling layer seemed to act as a secondary separating layer for those negatively charged or hydrophilic PhACs, but showed the cake enhanced concentration polarization effect for the neutral and hydrophobic ones. This study provides valuable insights for defining PhACs fate and NF membrane fouling behavior to fit increasingly stringent criteria for wastewater treatment.