Dimensional stability is one of the principal protection goals for waterlogged archaeological wood. Various materials, including natural resins, polyethylene glycol, sugars, glyoxal, etc., have been developed for dimensional stabilization of waterlogged archaeological wood upon drying. Recent studies demonstrated the excellent performance of organosilicon compounds, among which γ-mercaptopropyltriethoxysilane (MPTES) gave the best results. However, the interaction between MPTES and waterlogged archaeological wood has not been well explained. A further study on this topic might provide new insights into designing better consolidants for waterlogged archaeological wood. In this paper, archaeological pine wood (Pinus massoniana) from the Nanhai Ⅰ shipwreck was used as the research material, and the effectiveness of maintaining dimensional stability upon drying by MPTES and its mechanism are further explored and discussed through weight percentage gain, shrinkage, observation using SEM and FTIR techniques. The results show that:1) the samples treated by MPTES show desirable dimensional stability (3.5% volumetric shrinkage) and that the effectiveness of MPTES is confirmed at low weight percentage gains (around 50%); 2) the resultant silicone is distributed uniformly in cell walls rather than in cell lumina; 3) with an increase in treatment duration, the water content, or concentration, the absorption assigned to aryl ether decreased, which is negatively correlated to the weight percentage gains and related to the FTIR absorptions of silicone. On the basis of the above results, the reaction between mercapto group and lignin, as well as the consolidation mechanism of MPTES are discussed. It is proposed that the reaction between the mercapto group and lignin may be similar to the formation of organic sulfur in waterlogged archaeological wood buried in redox condition and the reaction mechanism of the initial step of the Kraft pulping process, which involves the formation of lignin quinone methides, catalyzed by acid or base, followed by the addition of mercapto groups, to form thioether structures. Due to the Si-OH and -SH groups in hydrolyzed MPTES, MPTES has multiple interactions with both lignin and cellulose, which help to build stronger interfacial bonding forces between wood components, and therefore increase the integrity and mechanical strength of waterlogged archaeological wood. In this study, the mechanism of dimensional stabilization of waterlogged archaeological wood upon drying after treatment with γ-mercaptopropyltriethoxysilane is proposed. It is further believed that introducing moderately reactive groups such as mercapto group can help increase the dimensional stabilization ability of WAW consolidating materials and may have promising research and application values in the future design and development of better materials for waterlogged archaeological wood protection.