Electrochemical hydrodesulfurization technology is a promising approach to remove sulfur compounds from fossil fuels, having the advantages of moderate operating condition, low energy consumption, and high automation. This method is still in the research and development stage, and the desulfurization efficiency needs to be improved. Here, we report an attempt to improve the desulfurization efficiency by increasing the active sites of catalysts. The amorphous MoS x are chosen as the catalysts and synthesized by the electrodeposition method at diffusionlimited conditions, which is regulated by either increasing the deposition potential or by adding glycerol into the electrolyte. With the decrease of chemical diffusion, the morphology of MoS x catalysts changes from continuous lamellae to dispersed nanoparticles on the surface of carbon cloth. Owing to the extensive exposure of the bridging sulfur groups S 2 2− and undercoordinated Mo(V) regions, the MoS x particles exhibit a more than two times increase of the desulfurization efficiency, reaching 22.5% in the electrochemical hydrodesulfurization. This study shows that structure optimization of catalysts by diffusion control is a facile and general strategy to improve reaction efficiency, which may be applied to various catalysts.