A novel three-dimensional (3D) manganese oxide (MnOX) hierarchical microflowers materials were prepared and applied to activate peroxymonosulfate (PMS) for the removal of phenol. The 3D α-MnO2 material exhibited higher catalytic activity than 3D Mn2O3 and 3D Mn3O4 materials, with 100% phenol removal within 60 min. The quenching experiment and EPR results indicated that 1O2 played a major role in removing phenol, SO4•–, O2•– and •OH ranked second. The kinetic studies indicated that the removal of phenol followed the pseudo-first-order kinetic model, and the reaction activation energy of 3D α-MnO2 material was 25.67 kJ mol−1. Besides, factors of 3D α-MnO2 catalytic performance such as catalyst dosage, PMS dose and reaction temperature were also investigated. This work provided a new approach for synthesizing 3D MnOX catalysts with high-performance and guidance for analyzing the catalytic activity of multivalent metal oxides.