The presence of humic substances as a component of natural organic matter (NOM) may cause inefficiency towards drinking water treatment processes, especially the membrane fouling during filtration process. Therefore, to enhance the efficiency of the conventional membrane filtration process, several copper doped Fe-N-C bimetallic heterogeneous Fenton-like catalysts (Cux@FeNC) were prepared and evaluated by executing their catalytic degradation performance against NOM. Results indicated that humic acid (HA, 10 mg/L) could be significantly degraded (95%) within 30 min application of Cu5p@FeNC-Fenton under neutral pH, which was relatively higher than of FeNC-Fenton (70%) under identical conditions. The macromolecular organic matters in NOM could be destroyed more effectively while the overall mineralization degree also became relatively higher. Meanwhile, a lower membrane fouling of UF (PES 20 kDa)/NF (DOW 270) and highest flux recovery after backwash were observed with Cu5p@FeNC-Fenton treatments. Characterization and chemical analysis further explored the introduction of Cux in FeNC was responsible for the rapid reactive oxygen species (ROS) generation and efficient degradation of NOM. Additionally, a possible copper-iron synergetic mechanism in Fenton-like system was proposed. This work gives a deep insight into the potential NOM degradation using Fenton-like Cux@FeNC catalysts and ensures the membrane fouling mitigation for effective water treatment processes.