Consolidation has always been a major conservation issue for waterlogged archaeological wood (WAW), which aims to prevent shrinkage and cracking upon drying. Here we developed a new organic solvent-free consolidation method using water-soluble amino silanes and dialdehydes, which involves versatile cross-linking processes between wood components and polysiloxane. Evaluations by shrinkage measurements after air-drying, Fourier transform infrared spectroscopy, static thermal dynamic analysis, and dynamic vapour sorption suggest the combination of N-(2-aminoethyl)-3-aminopropyltrimethoxysilane and glutaraldehyde provides the most satisfying dimensional stability, mechanical strength and hygroscopicity. The anti-shrinkage efficiency reached as high as 96.9% for highly degraded WAW of Catalpa sp. after air-drying. The bending strength was increased to approximately 4 times and the elastic modulus was increased by around 10 times. The described method provides a new solution for the consolidation and dehydration of WAW, which produces excellent dimensional stability in lab-scale trials after air-drying without using organic solvents. However, studies are required on the long-term stability of the materials and durability of the treated WAW against microbial and chemical degradation before it can be applied in practice.