In this study, we investigated the performance of powdered activated carbon dynamic membranes (PAC DMs) in fouling mitigation strategies during cross-flow microfiltration for high-efficiency seawater pretreatment. By altering the fouling mechanism and water molecule pathway, PAC DMs successfully enhanced the pseudo-steady-state filtration flux and rejection of cross-flow microfiltration by 53% and 29%, respectively, compared to filtration without a PAC DM. Moreover, Fenton oxidation processes (FOPs) application in the DMs’ cross-flow cleaning was studied and showed promising results, recovering up to 28% of the initial filtration flux when used alone and 52% when combined with alkaline cleaning. This study provides insight into the utilization FOPs cleaning technology for PAC DMs cross-flow cleaning, allowing the automation and optimization of DMs operation.