Using molecular dynamics simulations combined with the embedded atom method potential, we investigate the heating, cooling, and energetic reacting of core-shell structured Al-Cu nanoparticles. The thermodynamic properties and structure evolution during continuous heating and cooling processes are also investigated through the characterization of the total potential energy distribution, mean-square-distance and radial distribution function. Some behaviors related to nanometer scale Cu/Al functional particles are derived that two-way diffusion of Al and Cu atoms, glass phase formation for the fast cooling rate, and the crystal phase formation for the low cooling rate. Two-way atomic diffusion occurs first and causes the melting and alloying. In the final alloying structure, Cu and Al atoms mixed very well except for the outmost shell which has more Al atoms. For the investigation of the thermal stability and energetic reaction properties, our study show that a localized alloying reaction between the Al core and Cu shell is very slow when the initial temperature is lower than 600 K. But a two-stage reaction may occur when the initial temperature is 700 K. The reaction rate is determined by the solid-state diffusion of Al atoms in the Cu shell at the first stage, yet the reaction rate is much faster at the second stage, due to the alloying reaction between the liquid Al core and the Cu shell. At higher temperatures such as 800 K and 900 K, the alloying reaction occurs directly between the liquid Al core and the Cu shell.