In this work, we demonstrate a novel three-dimensional electro-Fenton system (3D-E-Fenton) for wastewater treatment with foam nickel, activated carbon fiber and Ti/RuO2–IrO2 as the particle electrodes, the cathode, and the anode respectively. This 3D-E-Fenton system could exhibit much higher rhodamine B removal efficiency (99%) than the counterpart three-dimensional electrochemical system (33%) and E-Fenton system (19%) at neutral pH in 30min. The degradation efficiency enhancement was attributed to much more hydroxyl radicals generated in the 3D-E-Fenton system because foam nickel particle electrodes could activate molecular oxygen to produce O2− via a single-electron transfer pathway to subsequently generate more H2O2 and hydroxyl radicals. This is the first observation of molecular oxygen activation over the particle electrodes in the three-dimensional electrochemical system. These interesting findings could provide some new insight on the development of high efficient E-Fenton system for wastewater treatment at neutral pH.