This work proposed a controllable synthesis of Ni-Mo catalyst supported inside multi-wall carbon nanotubes (CNTs). The results indicate that Ni improved the β-Mo2C formation and markedly promoted the benzofuran (BF) hydrogenation and hydrodeoxygenation activity of the catalysts. The synergistic interaction between Ni and Mo reached the maximum at a Ni/Mo molar ratio of 0.3, which could be favored by the proximity between the Ni and β-Mo2C particles inside the CNTs reaching a 99.5% of BF conversion to hydrogenated and deoxygenated products as 2,3-dihydrobenzofuran, octahydrobenzofuran, and ethylcyclohexane; in contrast, BF conversion on unsupported Ni-Mo2C-0.3 was only 0.7%. Deoxygenated products are favored under different conditions, such as the time, and mainly with the temperature achieving 93.8% of yield toward deoxygenated products with 100% of BF conversion at 320 °C. However, the catalyst activity is lost through reuse cycles, likely due to the deposition of high molecular weight compounds (coke) on the catalyst surface.