We study the adsorption of zigzag graphene nanoribbons (GNRs) on Si(001) substrates using the first-principles density functional theory, exploring the effects of the interface interaction on the structural and electronic properties of both GNRs and the substrate. By comparing the adsorption structures predicted by the local density approximation, the generalized gradient approximation, and the DFT-D2 approach, we confirm that both edge and inner C atoms of GNRs can form covalent bonds with the substrate. The GNR/substrate interaction destroys the antiferromagnetic coupling of the edge states in GNRs. The charge transfer from the substrate to GNRs exhibits a complicated pattern and is mainly localized near the C–Si bonds. We also observe a strong perturbation of the surface states and a surface reconstruction transition induced by the GNR adsorption.