Membrane fouling is one of the main drawbacks encountered during the practical application of membrane separation processes. Cleaning of a membrane is important to reduce fouling and improve membrane performance. Accordingly, an effective cleaning method is currently of crucial importance for membrane separation processes in water treatment. To clean the fouling and improve the overall efficiency of membranes, deep research on the cleaning procedures is needed. So far, physical, chemical, or combination techniques have been used for membrane cleaning. In the current work, we critically reviewed the fouling mechanisms affecting factors of fouling such as the size of particle or solute; membrane microstructure; the interactions between membrane, solute, and solvent; and porosity of the membrane and also examined cleaning methods of microfiltration (MF) membranes such as physical cleaning and chemical cleaning. Herein, we mainly focused on the chemical cleaning process. Factors affecting the chemical cleaning performance, including cleaning time, the concentration of chemical cleaning, and temperature of the cleaning process, were discussed in detail. This review is carried out to enable a better understanding of the membrane cleaning process for an effective membrane separation process.