Organosilicon materials have shown potential as dehydration agents for waterlogged wooden artifacts. These materials can polymerize under normal conditions to form polymers with favorable mechanical strength, antibacterial properties, and aging resistance. However, the insolubility of most organosilicon hindered their penetration into waterlogged wood, which may lead to an unwanted cracking. This study aimed to evaluate the effectiveness of polydimethylsiloxane (PDMS) and hydroxy-terminated polydimethylsiloxane (PDMS-OH) with low viscosity and moderate reactivity for dehydrating waterlogged wooden artifacts from the Nanhai No.1 shipwreck. Four surfactants ((3–aminopropyl) triethoxysilane (APTES), alkyl polyoxyethylene ether (APEO), tri-methylstearylammonium chloride (STAC), and fatty alcohol polyoxyethylene ether (AEO)) and cosurfactant were employed to transform the two kinds of water-repellent silicone oils into eight groups of highly permeable oil-in-water (O/W) emulsions. Under the catalysis of a neutral catalyst, in situ polymerization occurred within the wood cells. Group P2-2 formulated with PDMS-OH and APEO showed the best efficiency in maintaining the dimensions of the wood during dehydration. The dehydrated wood exhibited a natural color and texture with a minimal volume shrinkage rate of 1.89%. The resulting polymer adhered uniformly to the cell walls, effectively reinforcing the wood cell structure. The weight percent gain of the wood was only 218%, and the pores of the cell lumen were well maintained for future retreatment. This method effectively controlled the sol–gel reaction process of the organosilicon and prevented damage to the wooden artifact during the dehydration process. Moreover, the dehydrated wood samples only experienced a low weight gain of 17% at 95% relative humidity (RH), indicating their great environmental stability.