In this paper, N-doped carbon dots (NCDs) were successfully decorated on the spherical porous silica surface in deep eutectic solvents (DESs) as a novel class of green solvents. The appropriate density and hydrophility of DESs guaranteed the fine dispersibility of silica particles and NCDs, resulting in a homogeneous and thin layer of NCDs immobilization. As compared with traditional organic solvents (DMF and THF), higher surface coverage was obtained in the medium of DES, proving its feasibility as a new kind of alternative solvent for hydrophilic nanomaterial-based surface modification of silica spheres. The resulting NCDs-decorated silica particles (Sil-NCDs) were characterized in detail and packed into chromatographic columns to study their initial feasibility as adsorbent material for liquid chromatography. The resultant packing materials demonstrate a selective behavior for polar compounds in hydrophilic interaction liquid chromatography (HILIC) mode. This work gives a typical example of using carbon dots as stationary phase component, and such material is hopeful to be used in other research fields such as solid absorbents, recycling catalysts, and solid-state electrochemistry etc.