We explore the stability of matching boundary conditions in one space dimension, which were proposed recently for atomic simulations (Wang and Tang, Int. J. Numer. Mech. Eng., 93 (2013), pp. 1255–1285). For a finite segment of the linear harmonic chain, we construct explicit energy functionals that decay along with time. For a nonlinear atomic chain with its nonlinearity vanished around the boundaries, an energy functional is constructed for the first order matching boundary condition. Numerical verifications are also presented.