Recent studies on intramolecular junctions of silicon nanowires and carbon nanotubes have revealed a wealth of intriguing phenomena. However, the thermal properties of the intramolecular junctions of silicon nanowires (SiNWs) are not yet well understood. In this study periodic arrays of intramolecular junctions with different lattice orientations are investigated, and their thermal conductivities are calculated using nonequilibrium molecular dynamics (NEMD) simulations. Different from the X-shaped and Y-shaped junctions of carbon nanotubes, no distinct jump is found in the temperature profile at the junctions. Compared with straight pristine SiNWs of the same length, the thermal conductivity of the periodic array of intramolecular junctions is reduced. The underlying mechanism of the observed behavior is analyzed by the phonon spectral density of the atomic velocities. The dependence of temperature on the thermal conductivity of this junction array structure is discussed. (C) 2011 Elsevier B.V. All rights reserved.