Abstract Carbon nanotubes (CNTs) exhibit extremely high nanoscopic thermal/electrical transport and mechanical properties. However, the macroscopic properties of assembled CNTs are significantly lower than those of CNTs because of the boundary structure between the CNTs. Therefore, it is crucial to understand the relationship between the nanoscopic boundary structure in CNTs and the macroscopic properties of the assembled CNTs. Previous studies have shown that the nanoscopic phonon transport and macroscopic thermal transport in CNTs are improved by Joule annealing because of the improved boundary Van-der-Waals interactions between CNTs via the graphitization of amorphous carbon. In this study, we investigate the mechanical strength and thermal/electrical transport properties of CNT yarns with and without Joule annealing at various temperatures, analyzing the phenomena occurring at the boundaries of CNTs. The obtained experimental and theoretical results connect the nanoscopic boundary interaction of CNTs in CNT yarns and the macroscopic mechanical and transport properties of CNT yarns.