The UF membrane with molecular weight cutoff (MWCO) ranging from 2 kDa to 100 kDa and XAD-8 resin were employed to identify the characteristic of molecular weight (MW) distribution of wastewater effluent organic matter (EfOM) in terms of TOC and UV254, as well as the amounts of the hydrophilic/hydrophobic organic fractions in different MW ranges. Then, the nanofiltration (NF) membrane fouling experiments were carried out using the above fractionated water to investigate the effect of MW distribution and hydrophilic/hydrophobic characteristics of EfOM on the membrane flux decline using the fractionated water samples above. The experimental results have shown that 45.61% of the total organics belongs to the low MW one, among which the percentage of the hydrophilic organics with low MW (less than 2 kDa) was up to 28.07%, while that of the hydrophobic organics was 17.54%. In particular, the hydrophilic fraction was found to be the most abundant fraction in the effluents. MW distribution has a significant effect on the membrane fouling. When the MW was less than 30 kDa, the lower the MW, the larger was the specific flux decline, while in the case of MW higher than 30 kDa, the higher the MW, the larger was the specific flux decline, and the decline degree of low MW organics was larger than the high MW one. With the same MW distribution range, specific flux decline of the hydrophilic organic was considerably slower than that of the hydrophobic organic, which indicated that the hydrophobic organic fractions dominantly contribute to the flux decline.