Anaerobic hydrogen production in a continuous two-stage fermentation system was studied. Two continuously stirred tank reactors (CSTR) were employed to evaluate performances of the system. The first stage was fed with molasses wastewater, and the effluent discharged from the first stage was subsequently fed into the second stage. The hydrogen production rate (HPR) in the second stage achieved a remarkable increase from 1.76 L/d to 6.45 L/d during the operation by re-utilizing the residual substrates from the first reactor effluent. The two stages showed a similar metabolic pathway for biohydrogen fermentation. The hydrogen production yield (HY) and acidification efficiency increased markedly by more than 70% and 50% respectively, which indicated the hydrogen recovery and anaerobic acidification of organic substrates can be improved by the combined continuous two-stage hydrogen production process.