To improve hydrophobicity and thermal stability, polydimethysiloxane (PDMS) emulsion and silica sol were used for depositing organic/inorganic hybrid coatings in wood. PDMS emulsion could provide the hydrophobic film to improve the hydrophobicity and dimensional stability owing to its low-surface-energy. Silica sol could significantly enhance the surface hardness and thermal stability due to its penetration in cell walls, indicating the pore-filling effect in wood. Moreover, in the hybrid system, silica incorporation in PDMS emulsion helped to form integrate coatings in wood via Si-O-Si cross-linked networks. The hydrophobicity, surface hardness and thermal stability of treated wood were related to the loadings of silica sol in the PDMS. Stiff silica could compensate the negative effect on thermal stability caused by PDMS, and synergistically improve the surface hydrophobicity and hardness of wood. This work opens a facile method to produce bio-based materials with satisfied hydrophobicity and thermal stability to be used in humid environments.