The role of the interface roughness of Bi-Te core/shell nanowires is reported in reducing lattice thermal conductivity, which are prepared by on-film formation of nanowire (OFF-ON) that is capable of growing high-quality single-crystalline Bi nanowires, and by the subsequent sputtering of Te onto the Bi nanowires. The rough interface Bi-Te core/shell nanowires exhibit lower thermal conductivities than that of smooth interface counterparts, while electrical conductivities for these two types of nanowires are similar. We propose that the rough interface plays a pivotal role in suppressing phonon transport, which in turn, reduces thermal conductivity significantly.