The generation of hydrogen through water electrolysis is considered as a sustainable approach for future fuel production. Molybdenum (Mo)-based compounds are reported as highly active and inexpensive alternatives to platinum-based electrocatalysts for the hydrogen evolution reaction (HER). Currently, the major challenge for Mo-based HER electrocatalysts lies in establishing new concepts of micro-/nanostructure design to enhance the hydrogen evolution kinetics and realizing facile, large-scale, and green fabrication processes. Here, a fast, scalable, and eco-friendly metal-organic coordination precursor-assisted strategy is reported for synthesizing novel hierarchically mesoporous Mo-based carbon electrocatalysts for efficient hydrogen production. Benefiting from homogeneously distributed Mo-based nanocrystallites/heterojunctions and uniform mesopores, the Mo-based mesoporous electrocatalyst shows high hydrogen evolution activity and stability with a low overpotential of 222 mV at 100 mA cm −2 (Pt/C: 263 mV), ranging among the best non-noble metal HER catalysts in alkaline condition. Overall, the discovery of using dopamine-molybdate coordination precursor with silica nanoparticles will not only create a new pathway for controllable synthesis of diverse kinds of micro-/nanostructured Mo-based catalysts, but also take a step toward the fast and scale-up production of advanced mesoporous carbon electrodes for a broad range of applications.