This study investigated the performance of constructed wetlands coupled with microbial fuel cells (CW-MFCs) treating agricultural wastewater containing glyphosate (N-phosphonomethyl glycine, PMG), and the use of Cladophora as a cathode plant in this system. Ten devices were divided into Cladophora groups (CGs) and no Cladophora groups (NGs), with five PMG concentrations (0, 10, 25, 50, and 100 mg/L). PMG removal efficiency significantly decreased with increasing PMG (P < 0.01) and was higher in CG devices than in NG devices at low PMG concentrations (<50 mg/L). The removal efficiency of chemical oxygen demand (COD) and NH4+ in CGs was significantly higher than in NGs (P < 0.01). The highest power densities of 6.37 (CGs) and 6.26 mW/m2 (NGs) were obtained at 50 mg/L PMG, and the average voltage was significantly higher in CGs than in NGs (p < 0.01). Moreover, PMG had a negative effect on the enrichment of electrochemically active bacteria, but Cladophora could mitigate this effect. The abundance of the resistance gene epsps was stabilized; The phnJ gene increased with increasing PMG in NGs and was downregulated at high PMG concentration in CGs, indicating better microbial adaptation to PMG in CGs throughout the experiment.