Currently, the highly efficient conversion of biomass resources into highly valuable chemicals and biofuels is one of the most prospective approaches to reduce greenhouse gases emission and environmental pollution caused by excess consumption of fossil fuels. Herein, three-dimensional pompon-like well-defined RuCo particles with tunable crystallographic structures and surface atomically dispersed Ru atoms were constructed and intensively investigated as support-free metal catalysts in the hydrodeoxygenation (HDO) of lignin-derived guaiacol. It was demonstrated that the 300 °C-reduced RuCo sample possessed the hexagonal close-packed (hcp) crystallographic structure with surface abundant atomically dispersed Ru atoms, whereas 600 °C-reduced RuCo sample presented the face-centered cubic phase with lower surface Ru concentration. The as-fabricated RuCo-300 sample showed excellent catalytic HDO activity with a high cyclohexane yield of 85.3%. Comprehensive structural characterizations unveiled that the introduction of atomically dispersed Ru atoms into the RuCo-300 favored the formation of abundant surface Ru-Co sites, as well as electron-rich Ru0, and such-constructed Ru-Co sites were highly beneficial to the hydrogen dissociation on single Ru0 atoms and the further hydrogen spillover to adjacent Co0 atoms to promote the HDO process. Moreover, density functional theory (DFT) calculations revealed that the hcp structure of RuCo catalysts benefited the adsorption of guaiacol. The unique pompon-like microstructure of RuCo catalysts was conducive to the exposure of active sites and provided more open channels for the easy diffusion of reactants and products. Over the RuCo-300 catalyst, the guaiacol HDO could proceed rapidly via an initial demethoxylation reaction. The present Ru-Co synergetic catalysis in the structure of RuCo catalysts would provide a new strategy for constructing robust heterogeneous bimetal catalysts applied in practical HDO processes of a variety of lignin-derived phenolic compounds.