The interactions of complex organic matters in reclaimed water were studied for the rejection mechanisms for organics removal by nanofiltration (NF) membrane. Rejection study on single organic fractions showed that base fractions are the most difficult ones to be removed, with the removal efficiencies of 40.08–47.73% for hydrophobic-base (Hpo-B) and 75.51–79.14% for hydrophilic-base (Hpi-B), respectively. Experimental results for interaction studies showed that with the presence of hydrophilic-acid (Hpi-A) and hydrophobic-acid (Hpo-A) at a concentration ratio of 1, the average rejections for acid + base fractions were 11–30% and 9–26% higher than those for the two corresponding single fractions, respectively. It was noted that after the ratio reaches a certain range (>2 for Hpo-A in our case) the beneficial effects become less significant since the saturation of opportunities for interactions. With presence of acid and base fractions, the neutralization reactions and hydrophilic interactions would be the major beneficial interaction among different components. With the presence of hydrophobic-neutral (Hpo-N) at a concentration ratio of 1, the average rejections for neutral + base fractions were improved by 9–35% and when at a ratio of 2, the rejections only increased 2.28–8.87% more. The interaction between neutral organics and base organics would be due to the effect of coupling of different permeable components.