Electrocoagulation (EC) is an environmentally friendly and effective water treatment technique. It has been recently applied in combination with a filtration process. This study investigated the effects of an alternating pulse current (APC) on the electrodes, treatment efficiency, and energy consumption of an EC−filtration system during the treatment of mariculture tailwaters, from the aspects of current density and current conversion period (CCP), to generate ideas for improving the performance of the system. Results showed that using direct current (DC) would aggravate the electrode passivation, resulting in many white insoluble substances covering the surface of the electrodes. Moreover, the electrode passivation was more intense at a higher current density and longer system operation time (SOT). Significantly, the electrode weight increased by 1546.67 ± 54.50 mg when the system was operated for 90 min under DC at a current density of 45 A/m2. Unlike DC, APC significantly alleviated electrode passivation, enhanced the treatment efficiency, and reduced energy consumption. A shorter CCP produced better results. When the CCP was 1 min, current density was 45 A/m2, and SOT was 10 min, the removal efficiency of the EC−filtration system for total suspended solids (TSS), chemical oxygen demand (CODMn), and total nitrogen (TN) was 53.55 ± 1.66%, 47.76 ± 0.18%, and 15.55 ± 0.31%, respectively, and the energy consumption was 11.88 × 10−3 kWh/m3.