The buffering effect of citrate on biohydrogen production during corn stover fermentation by photosynthetic bacteria HAU-M1 was investigated. Specific concentrations of citric acid and sodium citrate were added to batch cultures, and the effects on hydrogen production and fermentation broth properties were analyzed. A maximum overall hydrogen yield of 78.26 mL/g corn stover were observed at citrate buffer concentration of 0.05 moL/L, increased by 32.54% relative to the blank group. At citrate buffer concentrations 0.05 moL/L, the effect on hydrogen yield with different pH values (5.5–7.5) of citrate buffer were explored. Maximum hydrogen yield 125.4 mL/g corn stalk was achieved at pH value of 6 and the final pH was effectively controlled. The results showed that pH value of fermentation broth was strongly affected by citrate buffer. The citrate buffer retarded the decrease of pH value of photo-fermentation broth, and significantly improved the biohydrogen production.