A facile, green and efficient microwave-assisted method was developed to oxidize cellulose hydrogel beads with neutral 2,2,6,6-tetramethylpiperidinyl-1-oxyl radical (TEMPO)-mediated system. Resulting cellulose beads were investigated by scanning electron microscopy, solid-state 13C-NMR spectra, and X-ray diffraction. The patterns of 13C-NMR spectra indicated that the oxidation occurred only at C6 primary hydroxyl carbon, and the carboxyl groups amounted to 1.28 mmol/g in the cellulose beads. The TEMPO-oxidized cellulose beads showed highly porous structures consisting of nano-sized fibrils with retention of original spherical shapes, and the crystallinity index of the cellulose II almost unchanged after oxidation. The maximum adsorption capacity of rhodamine B, auramine O, malachite green and methylene blue on the TEMPO-oxidized cellulose beads was found to be 609, 537, 740 and 873 mg/g, respectively, and the adsorption process was well described by pseudo-second-order kinetics. In addition, desorption tests showed that TEMPO-oxidized cellulose beads could be regenerated by acid treatment and used repeatedly. Thus, TEMPO-oxidized cellulose beads prepared by microwave irradiation can be potentially used for the removal of organic dyes from industrial wastewater.