Metal-free graphene-based catalysts have demonstrated excellent performance in advanced oxidation processes (AOPs). However, the recovery and reusability of these nanocatalysts are still a major issue. In this study, three dimensional (3D) nitrogen-doped reduced graphene oxide beads (NrGOb) were synthesized via a self-assembly method and then applied in heterogeneous activation of peroxymonosulfate (PMS) for the oxidation of hydroxybenzoic acid (HBA). The materials (NrGOb) were annealed at various temperatures ranging from 500 to 1000 °C, and the resulting NrGOb derived from 800 °C (NrGOb-800) exhibited the best performance for PMS activation. To avoid the challenging recovery, the degradation experiments were also performed in a packed-bed catalytic reactor. Various reaction parameters were investigated to optimize the efficiency of the system. Electron paramagnetic resonance (EPR) and quenching tests were carried out to differentiate the contribution of reactive radicals (SO4•- and •OH) in the degradation process and then aided in illustrating the degradation mechanism. Finally, the stability and reusability of the catalytic beads were investigated. The efficiency slightly declined with increased cycles; however, catalyst regeneration would be able to partially restore the active sites. The results suggest the feasibility of exploiting graphene-based macrostructures on the AOPs platform for the degradation of organic pollutants in commercial wastewater treatment plants.