Using the scattering matrix method, we investigate the thermal transport in a nanostructure at low temperatures. It is found that phonon transport exhibits some novel and interesting features: resonant transmission, resonant reflection, and small thermal conductance. A comparison between thermal conductances is performed when stress-free and hard-wall boundary conditions are applied for acoustic modes, respectively. The result indicates that the characteristics of the thermal conductance versus temperature for different types of boundary conditions are qualitatively different.