Errors and uncertainties are inevitable in the aerothermal data obtained from flight test of high-speed aircraft. It is of great significance to analyze and identify the sources of uncertainty and quantify the uncertainty for the reuse of aerothermal data in flight test, the reliability of numerical simulation and the correlation between flight and ground data.Firstly, based on the acquisition process of aerothermal data in flight test and the characteristics of flight test, the uncertainty sources of flight test data are analyzed and identified from the aspects of flight environment, tem-perature sensor measurement and heat-flux identification data processing. The uncertainty components caused by atmospheric parameters fluctuation and flight test measurement (including temperature sensor measurement and heat-flux identification data processing) are evaluated by non-intrusive polynomial chaos (NIPC) and Cramer-Rao bound combined with low-pass filtering method respectively. The synthetic standard uncertainty is obtained, and the uncertainty evaluation method of aerothermal data in flight test is established. Finally, taking the MF-1 flight test as an example, the uncertainty of the heat-flux measured at one of the measuring points (X = 400 mm, 0° meridian) at t = 19.48 s (when the flight Mach number reaches the maximum value) is given. The results show that the comprehensive uncertainty is about 11.43%, among which the uncertainty of aerodynamic heating data in-duced by flight environment factors is relatively larger, about 10.54%, while the uncertainty of heat-flux data caused by flight test measurement (including temperature sensor measurement and heat flow identification data processing) cannot be ignored, about 4.43%. In this study, the uncertainty evaluation method of aerothermal measurement data in high-speed flight test is preliminarily established, and the uncertainty evaluation example of aerothermal data is given, and the suggestions for reducing the uncertainty of aerothermal data are provided.