Despite the impressive advancements in nanoscale thermal metrology over the past decades, there are still some problems and challenges, including (1) how to eliminate the thermal contact resistance (TCR) error between the sensor and the sample for the resistive contact methods, (2) how to directly evaluate TCR at a single junction between nanostructures, and (3) how to efficiently establish the structure-property correlation for thermal transport at the nanoscale. In this study, we develop three in-situ thermal transport measurement methods in a scanning electron microscope (SEM) to address the above issues and focus on the measurement of thermal transport in one-dimensional (1D) materials. First, a method combining the electron beam (EB) heating in SEM with two suspended line-shaped heat flux sensors was developed to map the thermal resistance distribution along a 1D sample and further eliminate the TCR error at the sample-sensor junction in its thermal conductivity measurement. The in-situ thermal resistance mapping along a cup-stacked carbon nanotube (CNT) was performed using this method, from which the thermal conductivity of the CNT without the TCR error was extracted to be around 40 W/m·K and the TCR at the sample-sensor junction was measured to be 1.35 MΚ/W. Second, we developed a method for the in-situ and real-time measurement of TCR at a single junction between 1D samples in SEM. The contact condition can be dynamically and flexibly adjusted, and the TCR results can be studied in combination with the SEM-captured images of the contact morphology. Using this method, we measured the TCR between two multi-walled CNTs. Third, we developed a method to simultaneously measure the thermal conductivity and observe the internal structure of a 1D sample using scanning transmission electron microscopy in SEM for the structure-property correlation. The experimental results of two cup-stacked CNTs indicated that the sample with more structural disorders had a lower thermal conductivity. These SEM-based in-situ thermal measurement techniques will facilitate the elucidation of nanoscale heat transfer from the perspective of structure-property correlation.