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Summary: In this study, a CoNi/CoFe2O4 electrocatalyst with durian‐like structure was in‐suit fabricated on the conductive substrate of nickel foam using a hydrothermal method followed by a unipolar pulse electrodeposition (UPED), which was further applied for the production of hydrogen in a microbial electrolysis cell. The CoNi/CoFe2O4/NF electrode prepared with a pulse voltage of −1.2 V by the UPED exhibited the outstanding electrocatalytic activity and durability with the rate of hydrogen production achieved as high as 1.25 ± 0.0625 m3/(m3 day). The excellent performance of the electrocatalyst is attributed to the unique multilayer layered structure, which consisted of macroscopic porous NF, CoFe2O4 nanosheets, and CoNi double hydroxide nanosheets. The hierarchical architecture is binder‐free and beneficial for exposing catalytic active sites, enhancing mass transport, and large specific surface area for MEC hydrogen production. It is expected to the CoNi/CoFe2O4/NF composite electrode application in the practical microbial electrolysis cells to produce hydrogen during the treatment of wastewater. Highlights: A CoNi/CoFe2O4 electrocatalyst was prepared for microbial electrolysis cell.The electrocatalysts had unique multilevel hierarchical architecture.The electrocatalysts exhibited a high H2 production rate of 1.25 ± 0.0625 m3/(m3 day). [ABSTRACT FROM AUTHOR]