Nanofiltration (NF) membranes, especially polyamide (PA) ones, are widely applied in water treatment, food processing, and resource recovery thanks to their excellent separation selectivity to small solutes and high water permeability. However, membrane fouling is inevitable during the long-term operation and limits the large-scale applications of NF technology. Chemical cleaning is considered the most effective way to avoid fouling aggravation and quickly restore membrane permeability on site. However, frequent chemical cleaning would cause reversible/ irreversible changes in the physical and chemical properties of NF membranes, resulting in membrane damage and deterioration of separation performance. Moreover, the PA NF membrane with high selectivity and a relatively low cross-linking degree is more sensitive to chemical cleaning. Many efforts, therefore, have been dedicated to clarifying the effect of chemical cleaning on the NF membrane properties and its separation performance. This review summarizes recent developments in the field and epitomizes the synergistic/inhibitory effect among the chemical cleaning agents on the fouling removal. Besides the practical guides for chemical cleaning of the PA NF membrane, many opportunities to advance the field are also pointed out.