Hydrogen evolution reaction (HER), is considered as an ideal alternative approachs to settle the energy crisis. Therefore, we need to explore efficient and stable non-Pt-based electrocatalysts for hydrogen production from water electrolysis. In this work, S-doped ultrafine molybdenum carbide anchored on cellulose nanocrystals (CNC) derived carbon composite aerogels (Mo2C@S-CA) were synthesized for HER by a simple one-step carbonization method, utilizing inorganic-organic hybrid ammonium molybdate/CNC (AMM/CNC) as precursor. The obtained Mo2C@S-CA aerogels can not only provide plenty of active sites, but also accelerate the hydrogen release from the reaction surface of the electrocatalysts. The as-synthesized catalysts exhibit superior HER activity with a small overpotential value of 176 mV vs. RHE at 10 mA cm−2 and excellent long-term stability after 10,000 cycles in 0.5 M H2SO4. These superb properties make the catalyst be a promising electrocatalyst for the HER. This work highlights the importance of biomass-derived multifunctional value-added composite aerogels in enhancing the electrolysis of water.