Non-sulfided nickel-based catalysts with HNO3-pretreated CNT as support ((x1+x2) wt.% NiMe/CNT, xi represents metal loading amount, Me=Cu, Co, Mo) were synthesized, and introduced to the hydrogenation of synthetic bio-oil (acetic acid, furfural, hydroxyacetone and guaiacol mixtures) and aqueous fraction of bio-oil. Synthetic bio-oil was chosen for the screening of catalysts. Results showed metal synergistic effect would improve the catalysts activity, and reduced (15+5)wt.% NiMo/CNT exhibited better catalytic activity with higher amount of alcohol compounds (up to 61.8%) and fewer undesirable compounds with low H/Ceff. An obvious aldol condensation between furfural and hydroxyacetone was observed to give a C8 compound, which could give most valuable hydrocarbon after deep hydrogenation. The hydrogenation of aqueous fraction of bio-oil over NiCu/CNT, NiCo/CNT, NiMo/CNT showed different catalytic activity for the conversion of compounds with low H/Ceff to alcohols, and the alcohol compound amount over NiMo/CNT after reaction was up to 63.9%.