The effect of stirring (200–800 rpm) on the synergistic fermentation hydrogen production by bicellular system consisted of Bacillus cereus (A) and Brevundimonas naejangsanensis (B) was investigated. Results indicated that hydrogen yield is the highest (1.36 mol H2/mol glucose) at 800 rpm for bicellular system and its efficiency is 1.3 and 1.4 times higher than the highest value obtained from the single fermentation of Strain A at 800 rpm and Strain B at 400 rpm, respectively. Butyric acid-type fermentation is dominated during the co-cultured fermentation at preferred stirring speed. Results via computational fluid dynamics (CFD) simulations showed that the area-weighted average value of velocity (m/s) on the cross section (y = 4.365 mm) is 0.104, 0.198 and 0.358 for the co-cultured fermentation under different stirring speeds, respectively. Major hydrodynamic parameters increased with the increasing stirring speed. This preliminarily revealed that hydrogen yield is seriously limited by the main accumulated metabolites.