The bimetallic nanothermites, composed often of the core-shell nanoparticles or the nano-scale multilayers, provide a direct interface between two reactive metals and therefore facilitate the thermite reaction without generating excessive gases. This characteristic is extremely important for wire or material joining applications. In this study we investigated the energetic properties and diffusion characteristics of bimetallic atoms in the Al/Pd core-shell nanoparticles. A classic molecular dynamics approach was implemented using a recently reported force field for the Al/Pd binary system. The results suggested that, in order to preserve the core-shell structure of the Al/Pd nanoparticle before being utilized for the material joining purpose, it is essential to maintain an isothermal condition at a lower temperature such as 150K. In addition, a thicker Pd shell will further hinder the diffusion processes within the core-shell nanoparticle.