A two-phase anaerobic system comprised of upflow anaerobic sludge bed (UASB) reactor for hydrogen production and internal circulation reactor (IC) for methane production was proposed and investigated at laboratory scale and mesophilic temperature (35 °C). Hydrogen was efficiently produced from the UASB with the highest production rate of 3.00 ± 0.04 L · L−1reactor · d−1 at optimum hydraulic retention time (HRT) of 6 h and in the IC, methane was also produced from residual organic matter and soluble metabolite products (SMP) with a production rate of 2.54 ± 0.04 L · L−1reactor · d−1 at optimum HRT of 15 h. Finally, system HRT of 21 h was determined to be the optimum HRT at which energy conversion efficiency increased from 9.6 ± 0.1% (hydrogen only production) to 72.4 ± 2.5% (hydrogen and methane coproduction) and system chemical oxygen demand (COD) removal reached up to the high level of 90.1 ± 2.1%.