Direct energy harvesting from the newly established constructed wetland-microbial fuel cell (CW-MFC) offers it a competitive position compared with traditional constructed wetlands (CWs) to allow the CWs for wastewater treatment and concomitantly achieve power generation. However, the integration of MFC into CWs always faces a large portion of energy losses due to the existence of higher internal resistance. This paper reports tests of a novel strategy, namely a capacitator engaged duty cycling (CDC) strategy, to harvest energy from an open air bio-cathode CW-MFC. Results show that with duty cycle value of 31.6% (D = 31.6%), the effective charge obtained from CDC strategy is 19.81% higher than the conventional continuous loading (CL) mode within the same discharging time. With a lower D value of 20% (D = 20%), the total charge harvested increased about 25.0%. The CDC operation mode shows advantages over the higher internal resistance system and contributes to a higher normalized COD removal rate. This operation strategy can minimize the energy losses with a suitable D value. It is a simple but effective way to maximize the energy harvesting from the CW-MFC system.