The chemical heat sink of endothermic hydrocarbon fuels (EHFs) is generally dependent on its thermal cracking in the cooling channel, which is accompanied and limited by the formation of carbon deposit. In this work, HF-1 (a kerosene based EHF) was electrically heated in the rectangular, square, and circular channels with the same cross-sectional area under 3.5 MPa to study the effect of cooling channel geometric structures on the thermal cracking and carbon deposition behaviors. It was found that under similar conditions (inlet flow rate of fuel, pressure, outlet temperature), conversions of HF-1 in both rectangular and square channels were slightly higher than that in the circular one with high selectivity to methane but lower selectivities to the primary cracking products (such as 1-hexene and 1-heptene, etc.). In addition, more carbon deposits were formed in the rectangular and square channels, especially around the corners of channels. Based on the CFD simulation, the possible reasons should be ascribed to the difference in the gradient uniformity near the wall of different channels. The higher temperature and lower velocity in the boundary layer of the quadratic channels might cause the thermal cracking to be slightly severer and the rapid secondary reactions to form carbon deposit.