This article provides a systematic study on the resorcinol-formaldehyde (RF) resin coating via a sol-gel process with focus on surface modification of the core. With colloidal SiO2 particles as the model core material, diverse surface modification methods were investigated to verify the feasibility of subsequent RF coating process. It is confirmed that the RF coating is strongly influenced by surface charge of the SiO2 core, which can be adjusted by suitable surface modification. Both cationic surfactant and amino functional group can modify the silica surface with positive charge, and it is readily coated with the negatively charged RF resin. The primary amine surfactant with positive charge fails to induce the RF coating onto the SiO2 particles, which may be due to the relatively weak interaction between the surfactant and silica. In addition, the negatively charged sulfydryl functionalization also contributes to a successful coating probably through the gathering of cationic ions around the core. The RF coating process has opened a versatile avenue for the construction of yolk-shell carbon-encapsulated nanocomposites. Catalytic tests indicate that the catalytic performances of the synthesized nanocomposites depend strongly on the method of synthesis.