Measurements of transport phenomena are constantly plagued by contact resistance, prohibiting the sample's intrinsic electrical or thermal conductivity from being accurately determined. This predicament is particularly severe in thermal transport measurements due to the inability to meet similar impedance requirements for a four-probe method used in electrical resistance measurements. Here, we invent a three-probe measurement method that makes an accurate determination of thermal conductivity possible for nanomaterials. Incorporating electron beam heating provided by a scanning electron microscope (SEM) on a diffusive thermal conductor not only quantifies the thermal contact resistance, which may introduce an error of more than 270% to a sample's thermal conductivity, but also eliminates several device uncertainties that may contribute an additional 17% error in a measurement. The method also enables local temperature measurements, revealing nanoscale structural variations unfound by SEM. The high accuracy of the technique would make standardization of nanoscale thermal transport measurement possible.