Pre-treatment of biomass prior to fermentation can effectively boost gaseous biofuel production. However, inhibitors including furfural and vanillin can be generated from the hydrolysis of biomass such as lignocellulosic biomass and algae. In this study, the inhibitory effects of furfural and vanillin on two-stage fermentative hydrogen and methane co-production were assessed. The results showed that vanillin exhibited stronger inhibition than furfural under the same concentration. In first stage hydrogen fermentation, the minimum hydrogen yield of 188.5 mL/g(glucose) and hydrogen production rate of 3.8 mL/g(glucose)/h were obtained from 4 g/L vanillin addition, with the maximum delay of fermentation peak time (more than 48 h). Furfural could be completely degraded to furfuralcohol within 12-48 h fermentation. In contrast, around 1.5%-53.5% of vanillin remained unconverted after 96 h fermentation. Two-stage process significantly mitigated the inhibition on subsequent methane production. Compared with direct methane fermentation, the methane yields increased by 105%-263%, whereas the methane production rate increased by 78.5%-204%. Inhibitors would suppress the production of volatile fatty acids and alter the metabolic pathways, resulting in a large deviation on the chemical oxygen demand balance (from -63.9% to -17.7%). The final energy conversion efficiency (from 31% to 89%) also decreased with increasing inhibitor concentration.