• Electrostatic LBL self-assembly strategy is firstly employed to integrate MoS 2 with CMOF. • Superior rejection rates are increased above 27–55% more than that of monomer membranes for FQs. • Synergy of size exclusion, electrostatic repulsion, and hydrophilic interaction is explained. • High stability in harsh environments for 72 h and over 90% rejection against FQs in the real sample. Developing a novel nanofiltration membrane for effectively purifying antibiotic wastewater has been a daunting challenge in recent years. However, a convenient and controllable strategy for constructing membranes with two-dimensional nanomaterials (2DNMs) and metal–organic frameworks (MOFs) needs to be further studied. Herein, a loosely hierarchical architecture composite membrane has been fabricated, utilizing an electrostatic layer-by-layer (LBL) self-assembly method to intercalate chitosan crosslinked UiO-66-NH 2 MOFs (CMOF) into MoS 2 laminates. Through regulating the CMOF content, lower hydraulic-resisted channels and precise separation regions have been formed in the hierarchical architecture. The well-designed MoS 2 /CMOF composite membrane exhibited enhanced water permeance (78.98 ± 1.45 L·m -2 h −1 bar −1 ) and superior antibiotic rejection capability (98.01 ± 1.12% for ciprofloxacin and 94.31 ± 0.68% for ofloxacin), which are increased by 27–55% more than monomer membranes. Detailed analysis results indicate the nanofiltration performance of the MoS 2 /CMOF composite membrane depends heavily on the synergistic mechanism, including the molecular sieving effect (size exclusion), electrostatic repulsion, and hydrophilic-hydrophobic interaction. Besides, the MoS 2 /CMOF composite membrane has emerged with excellent antifouling ability and long-term stability, which could maintain favorable rejection efficiency in continuous nanofiltration for 72 h under an alkaline and acidic environment. Furthermore, it presents over 90% antibiotic rejection rates for real water samples obtained from the municipal domestic sewage and livestock wastewater along the Xiangjiang River in China, indicating its good availability. In general, this work provides a new vision and a reasonable design strategy to construct 2DNMs/MOFs-based nanofiltration membranes with hierarchical architecture, further expanding their application in wastewater treatment and reclamation, in harmony with the global trend of green and low-carbon development.