Modulating the electronic characteristics of catalysts plays a significant role in optimizing their catalytic activity. Herein, Mn-doped nickel molybdate (MNMO) nanorods are synthesized via replacing the partial Ni sites by the Mn element, engineering a bimetallic synergistic effect to enhance the activation of oxygen (O2). Compared with the extremely low catalytic activity of pristine nickel molybdate (NiMoO4), complete desulfurization can be achieved by MNMO under the same reaction conditions. Characterization results show that the electronic structure and surface atomic composition of pure NiMoO4 will be modulated owing to the introduction of Mn atoms, leading to the enhancement of the oxygen vacancy content and stronger O2 activation capacity. Besides, the optimized catalyst MNMO-20 also displays satisfactory cycle performance, and the sulfur removal of dibenzothiophene still maintains 96.1% after six times of recycling. The distinctive engineering strategy and simple synthesis method provide a new insight in designing and developing oxidative desulfurization catalysts with high stability and effectivity.