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Despite the fact that epoxy has continuously used as encapsulant in electronic packaging, its joint with copper-based substrate is prone to delaminate during reliability test. A prime reason is the lack of adhesion between Cu and epoxy compound. To solve the problem, self-assembly molecular structure (SAM) is adopted to improve adhesion of epoxy-copper system. In seeing that hydrophobic behaviour of the SAM structure may hinder moisture diffusion along the interface, further work in terms of the molecular structure of the SAM candidates is conducted in this study. This work aims at investigating the moisture effect on the interfacial adhesion with different types of SAM modified interfaces through molecular dynamic (MD) simulations. This study uses MD model as a tool to 1) predict the interfacial adhesion of the SAM modified interface in moisture sensitive condition; 2) investigate the moisture diffusion behavior of the modified interfaces under moisture sensitive conditions. The results demonstrate a reasonable qualitative corelation between the MD prediction and the TDCB tested data. Nevertheless, without the experimental adsorption data for the SAM material, the moisture diffusion coefficient obtained from MD study cannot explain the adhesion degradation after aging.