The creation of non-noble metal magnetically-separable heterogeneous catalysts for the hydrodeoxygenation of biomass to value-added products has received substantial attention. Herein, we report a facile synthesis of magnetically-separable cobalt catalyst embedded in hierarchically porous N-doped carbon nanospheres (Co@NC) by in situ non-noble metal nitrate-promoted pyrolysis reduction strategy using nitrogen/oxygen co-doped resin polymer spheres as precursors. The facile H2O2 post-treatment process increased surface oxygen-containing groups and improved hydrophilicity to disperse catalysts in aqueous solutions. Moreover, owing to the non-noble metal nanoparticles coated with a graphitic nitrogen-doped carbon layer, the as-prepared Co@NCH2O2 catalyst exhibits excellent catalytic activity and stability of vanillin hydrodeoxygenation in aqueous solutions. This strategy can be extended to other non-noble metal nitrates like M@NCH2O2 (M = Co, Ni) within good recyclability, magnetically-separable ability, and general applicability for a broad substrate scope, further highlighting the superiority of our active catalysts.