An innovative multistage anaerobic hythane reactor (MAHR) which combines an internal biofilm (MH) and an external up-flow sludge blanket (MM) was proposed to produce biohythane from wastewater. The effect of pH on its biohythane production and microbial diversity was performed. Results showed that the maximum hydrogen production rate (4.900 L/L/d) was achieved at a pH of 6.0, in comparison to a maximum methane production rate of 10.271 L/L/d at a pH of 6.5. In addition, a suitable hythane (H2/(H2+CH4) of 16.06%) production can be achieved in MH after the initial pH was adjusted from 7.0 to 6.5, and a relatively high methane yield (271.34 mL CH4/gCOD) was obtained in MM. Illumina Miseq sequencing results revealed that decreasing pH led to an increase of the acidogenesis families (Eubacteriaceae, Ruminococcaceae) in MH and an increase of hydrogenotrophic methanogens (Methanobacteriaceae) in MM. The Methanosaetaceae gradually occupied a major portion after a long period of recovery. This work demonstrated the unique advantages of MAHR for the biohythane production under optimal pH conditions.