We propose a specialized gate-drain separation structure for use in investigation of the dynamic behavior of the thermal transport characteristics in AlGaN/AlN/GaN heterojunction transistors. Using this structure, the influence of the two-dimensional electron gas (2DEG) on the horizontal heat transfer in these transistors was identified experimentally. A temperature delay (i.e., the difference in temperature at the same time) of 1.3 degrees C, which accounts for 8.6% of the total temperature rise, was calculated to be caused by a 0.3 pm x 150 mu m 2DEG depleted region. In addition, the temperature transients show that the 2DEG can accelerate the temperature to the steady state. Infrared measurements were also carried out to benchmark the results. In particular, the sample structure allows the measurement of a complete thermal process that includes both heating and cooling without interruption. Based on a comparison of the two processes, we demonstrated and corrected an error in the temperature rise that occurred when the Schottky junction voltage was used as the temperature-sensitive parameter.