Abstract: For flight vehicles operating in high-altitude rarefied flow regimes, the surface heat flux levels are relatively low due to the reduced density of the surrounding atmosphere. However, prolonged cumulative heating over extended flight durations can still generate significant thermal loads, which should not be neglected in engineering practice. Therefore, the precise measurement of minute heat fluxes is critically important for ensuring flight safety, enabling refined thermal design, optimizing aerodynamic performance, and enhancing overall system reliability. In this study, a flat plate model is employed to systematically investigate various heat flux measurement techniques within a hypersonic low-density wind tunnel. Both point measurement methods—including dual-junction coaxial thermocouples, integrated thermocouples, and thin-wall calorimeters—and surface measurement techniques such as infrared thermography and phosphorescence thermography were quantitatively evaluated under rarefied aerodynamic heating conditions. Furthermore, a heat flux identification method based on reference junction temperature correction is proposed specifically for dual-junction coaxial thermocouples applied in long-running intermittent low-density wind tunnels. The experimental results demonstrate that applying reference junction temperature correction effectively extends the valid measurement duration and improves the measurement accuracy of coaxial thermocouples in such facilities. It is also found that conventional phosphorescence coatings exhibit limited sensitivity when the heat flux falls below 1 kW/m², which necessitates the future development of higher-sensitivity coating materials. Traditional aerodynamic heat measurement techniques remain applicable under rarefied inflow conditions, provided that strict adherence to the one-dimensional semi-infinite assumption is maintained. To minimize lateral heat transfer effects while preserving an adequate sensor signal-to-noise ratio, the heating time of the model should be kept as short as possible. Finally, the heat flux data obtained from all five measurement techniques agree well with the results of direct simulation Monte Carlo (DSMC) simulations. These DSMC results provide valid flat-plate benchmark heat flux data for algorithm verification under rarefied hypersonic inflow conditions at altitudes above 70 km.