Thermally conductive nanomaterials hold great promise for applications in thermal management. However, the interfaces between nanomaterials can significantly impede heat flow, and a comprehensive understanding of thermal transport across nanoscale contacts is highly desired. Here, by integrating a movable nano-manipulator within an electron microscope with a nanofabricated thermal sensor, we adjusted the contact positions, overlapping length, and crossing angles between two carbon nanotubes (CNTs) as desired, while concurrently measuring the thermal contact resistance (TCR) at the van der Waals junction. The TCR far surpassed that of the studied 6 μm-long CNTs, particularly in contacts affected by inevitable nanoscale surface contamination. The TCR per unit area exhibited significant variations across different contact morphologies, spanning two orders of magnitude even for identical pairs of samples, attributable to structural non-uniformity within the CNTs. This in-situ approach and the notable morphology effects can guide the control of heat at the nanoscale.