Constructed wetlands (CWs), a cost-effective and eco-friendly wastewater treatment technology, are extensively applied in various types of wastewater treatment. There is a series of strong impacts on CWs performance by the accumulation of clogging matters which attribute to physical, chemical, and biological processes after the long-term operation. This paper summarizes the mechanism of clogging formation, which can be classified into physical, chemical, and biological clogging. Moreover, it analyzes the typical measures for preventing and controlling clogging in CWs. The integration of bioelectrochemical systems (BES), including microbial fuel cells (MFCs) and microbial electrolysis cells (MECs) into CWs is proposed as a safe and efficient way to alleviate substrate clogging on-site, owing to the fact that BES can easily automate the control or adjustment of its internal electric field form. The mechanism of clogging control by CW-BES is comprehensively described and analyzed. With the help of BES, the clogging substances obtained optimized occurrence form, reduced hydrophobicity and advantageous spatial distribution. Besides, the microbial community achieved promoted structure, accelerated rates of electron transfer and more diverse metabolic pathway. Compared to traditional methods for evaluating the clogging of CWs, the MFC sensor offers the advantages of being fast, enabling in-site detection, and being non-destructive. Future research should be focused on the theoretical underpinnings for putting CW-BES into practical use. Additional, efforts should be made to ensure the stable, long-term operation of CWs.