To ensure the conservation of waterlogged archaeological wood, sustainable, safe, and effective methods must be implemented, with consolidation and dehydration being crucial for long-term preservation to maintain dimensional stability and structural integrity. This study compares the permeability of 45% methyltrimethoxysilane (MTMS) and 45% trehalose solutions to evaluate the dimensional changes, hygroscopicity, and mechanical properties of treated wood. Since the collected samples (from an ancient ship, Luoyang Canal No. 1) were mildly degraded, the drying method had a slight impact on the properties of archaeological wood. Consolidated with trehalose and MTMS agents, the longitudinal compressive strength of the waterlogged wood’s cell walls increased by 66.8% and 23.5%, respectively. Trehalose proved to be more advantageous in filling pores and reducing overall shrinkage, while MTMS significantly reduced the hygroscopicity and surface hydrophilicity of the wood substance. Overall, the MTMS treatment has a smaller effect on the appearance of samples, making it more suitable for the consolidation of mildly degraded waterlogged archaeological wood.