Heterogeneous nanostructures involve nanoscale interfaces with different materials components, such as matrix and fillers in composites, stacking planer structures in electronics, and aggregates of nanomaterials. Thermal transport in heterogenous nanostructures is critical to the safety and performance of various applications ranging from high temperature turbines, microelectronics, solar cells, thermoelectrics, buildings’ thermal management and so on. However, it remains challenging to achieve rational control of the thermal properties in heterogeneous nanostructures due to limitations in current characterization techniques and fundamental understandings of interface thermal transport. My PhD research focuses on developing new thermal measurement techniques and investigating fundamental interface transport mechanisms through the combination of experiments and modeling, to provide rational control over heterogeneous nanostructures for better addressing practical heat management and energy conversion problems using nanoengineering. The study of thermal transport in heterogeneous nanostructures in my dissertation spans from technical development of new tools, experimental measurements at nanoscale interfaces and porous structures, and atomistic modelling of fundamental transport physics to practical device applications. First, I have developed a new metrology based on asymmetric beam time-domain thermoreflectance (AB-TDTR) that enables accurate measurements over three-dimensional thermal transport. Through the design of an asymmetric laser beam with controlled elliptical ratio and spot size, the experimental signals can be exploited to be dominantly sensitive to measure anisotropic thermal conductivity along the cross-plane or any specific in-plane directions. I have further applied this new approach to investigate anisotropic transport phenomena that enables unique applications. Second, I have explored the effects of crystal orientations and dipole-dipole interactions on interface thermal transport. In particular, for the first time, we have observed a record-high anisotropy ratio of 3.25 in the thermal boundary resistance across a prototype two-dimensional material, i.e., black phosphorus. Moreover, my study has resulted in the first observation of strong effects from long-range molecular dipole-dipole interactions on interface thermal transport. In addition, I have also investigated the heterogeneous integration of our recently developed new high thermal conductivity materials with prototyped high-power semiconductor, i.e., gallium nitride. Our in-situ measurement demonstrated substantially reduced hot-spot temperatures in devices using boron arsenide cooling substrates, beyond the best state-of-the-art HEMTs using diamond or silicon carbide. Lastly, I have investigated thermal transport in porous and mesoporous structures, including super-hydrophobic polymer aerogel, transparent mesoporous silica, and flexible tin selenide nanosheet films for applications in buildings, windows, and thermoelectric energy conversion.