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Atomically dispersed cluster catalysts own versatile applications in biomass valorization, while the controllable assembly and microenvironmental regulation remain a crucial challenge. Herein, Co clusters assembled via nanosized ZIF-67 sprouted from Co-Al layered double hydroxide nanoflowers were applied for selective hydrogenation of furfural (FAL). The pyrolysis temperature can tune the microstructures and acid properties of the catalyst, which accounts for the hydrogenation of FAL to furfuryl alcohol (FOL), 2-methylfuran (2-MF), and tetrahydrofurfuryl alcohol (THFOL) with yield of 99.1 %, 96.7 %, and 82.3 %, respectively. The Co clusters favor C O bond adsorption via bridging-type adsorption mode while suppressing the furan ring adsorption. Moreover, ultra-dispersed Co clusters facilitate the cleavage of C-OH bonds in FOL intermediate, leading to a high 2-MF yield. As the pyrolysis temperature increase, the formed Co nanoparticles are conducive to the parallel adsorption of FAL, resulting in the production of THFOL. This work affords a multi-functional catalyst in catalytic biomass upgrading. [Display omitted] • The ultrafine Co clusters embedded in carbon matrix were developed. • The migration of Co on LDH surface will expose a large number of Lewis acid sites, which facilitate the activation of C=O band. • The microstructure and acid-base properties can be adjusted by varying the pyrolysis conditions. • The relationship between the adsorption mode of substrate and the hydrogenation pathway was thoroughly explored. [ABSTRACT FROM AUTHOR]