The thermal transport properties of self-organized Ge nanostructures on Si were studied by means of ultrafast surface sensitive time-resolved electron diffraction. The thermal boundary resistance was determined from the temperature response of the Ge nanostructures upon impulsive heating by fs-laser pulses. The transient temperature was determined through the Debye–Waller effect. Epitaxial growth of Ge hut and dome clusters was achieved by in-situ deposition of 8 monolayers of Ge on Si(001) at 550 °C under ultra-high vacuum conditions. Time-resolved spot profile analysis of different orders of diffraction spots was used to distinguish between the thermal response of hut and dome clusters. Dome clusters of 6 nm height and 50 nm width cool with a time constant of tau = 150ps which agrees well with numerical simulations calculated in the framework of the diffuse mismatch model. The much smaller hut clusters with a height of 2.3 nm and width of 23 nm exhibit a cooling time of tau = 55 ps , which is a factor of 2 slower than predicted by theory.