Abstract: It is common and unavoidable that constructed wetland bio-clogging is caused by the massive secretion of Extracellular Polymeric Substances (EPS) of microorganisms. Bio-electrochemical Systems (BES) using additional electric fields or self-generated electric fields can promote the dispersion, degradation and utilization of EPS, and can control and alleviate the bio-clogging of constructed wetlands to a certain extent. Therefore, in this study, two bio-electrochemical systems, CW-MEC and CW-MFC, were used to intervene in constructed wetlands in different bio-clogging periods. Removals of COD and nitrogen and the content of stratified EPS in the vertical direction were used to evaluate the mitigation ability of the two BES systems to bio-clogging at different intervention timings. The results indicated that the two BES systems showed good clogging mitigation effect. Intervention before clogging, the CW-MFC system can well maintain the removal effect of pollutants COD and TN (91.4%—61.3% and 65%—40%) and increase the water output rate (the change rate is 67.6% in the CW group). The CW-MEC system can significantly reduce the EPS content of the upper layer, restore the porosity of the system, and have a better effect of relieving clogging. Both of these two BES have good in situ application potential in alleviating bio-clogging in constructed wetlands, which provides reference for the effective prevention and control of bio-clogging in constructed wetlands during different periods.