Si3N4 and SiO2 have been widely used in lithium batteries and optical devices. The high energy density brought by device integration makes the interfacial heat transport at the nano scale a hot spot. To optimize interfacial heat transfer, the roughness of the device surface is continuously reduced down to the nanometer. However, due to the limitation of spatial resolution, it is difficult to realize the measurement of thermal boundary resistance in the case of nanoscale contact by the existing measurement means. There is a great discrepancy between the measurement and simulation results, making the optimization of interfacial heat transfer lack of experimental verification. In this paper, the measurement of thermal boundary resistance of Si3N4/SiO2 interface at the nano-scale, was firstly realized by the optimized 3ω-SThM system. The effect of air tunnel on the heat transfer between real surfaces was also analyzed. The progress made so far provides an effective experimental tool to measure interfacial heat transport at nanoscale point contact.