Anomalous heat conduction in low dimensional materials shows divergent thermal conductivity with increasing characteristic length, which brings many opportunities in thermal management applications and unexplored phonon transport mechanisms. The molecular heterojunctions, consisting of an interface that is formed by different lattices, exhibit unique physical properties especially thermal rectification phenomenon. In this work, we investigate the heat conduction across a one-dimensional heterojunction bridging a carbon nanotube (CNT) and a boron nitride nanotube (BNNT). The molecular dynamic (MD) simulation shows that the rectification ratio is as high as 8.9 in a 300-nm system at/above the room temperature, which is due to the asymmetric interfacial thermal conductance in the opposite directions of heat flow. The interfacial thermal conductance (G) obeys the length dependence of G ∝ Lβ, presenting a divergent and convergent behaviors of anomalous heat conduction that was only reported for homogeneous materials. By analyzing the length-dependent and temperature-dependent phonon density of state, this anomalous interfacial heat conduction can be explained by the Kapitza resistance model and the population of frequency-dependent phonons. Further calculation of mean square displacement of atoms validates the superdiffusion and subdiffusion behavior of the interfacial conductance. This result demonstrates the superb capability of the one-dimensional heterojunction to control phonon transport, which could be used as the basic element of high-efficient and intelligent thermal management devices.