Wood is a green and renewable bio-based building material, but its hygroscopicity affects its dimensional stability, limiting its use in construction. Chemical modification can improve its properties, yet its effectiveness depends on wood permeability and traditional modifiers. This study first used a deep eutectic solvent (DES) to boost the permeability of North American alder wood. Then, methyl trimethoxysilane was impregnated under supercritical carbon dioxide (SCI), pressure (PI), vacuum (VI), and atmospheric pressure (AI) conditions. DES treatment damaged the cell structure, increasing wood permeability. Silane was deposited and polymerized in the cell lumen, chemically bonding with cell-wall components, filling walls and pits, and thickening walls. The VI group had the highest absolute density (0.59 g/cm³, +36.6%) and the lowest moisture absorption (4.4%, −33.3%). The AI group had the highest ASE (25%). The PI group showed the highest surface hardness (RL, 2592 N) and a water contact angle of 131.9°, much higher than natural wood. Overall, the VI group had the best performance. Silane reacts with cellulose, hemicellulose, and lignin in wood via hydrolysis and hydroxyl bonding, forming stable bonds that enhance the treated wood’s hydrophobicity, dimensional stability, and surface hardness.