Pilot-scale H2 fermenter using food waste as a substrate was operated at various weight C/N ratios (20, 25 and 30) and alkaline shock treatment method was applied to recover the performance. At C/N ratio 20, 183.9 L of H2 was produced per day which was equivalent to 4.4% conversion of total added carbohydrate on COD basis. C/N ratio higher than 20 showed decreased performance accompanied by the increase of lactate and propionate production. Alkaline shock treatment method was so effective that H2 production was almost doubled up. Also, settling characteristics of H2 fermenter was investigated using RNA assay and the method to increase the H2 production was suggested.