Flight test is an important way to obtain the aerodynamic parameters of reentry capsule under real flight conditions. The results of aerodynamic parameters identification play an important role in the evaluation of CFD and wind tunnel experimental data, and in the improvement of aerodynamic design. For the lunar-earth high-speed reentry, the aerodynamic environments are complex, the aerodynamic predictions are difficult, and the results are very uncertain. Therefore, it is very necessary to give the deviations of aerodynamic identification results. Otherwise the aerodynamic data are useless for aircraft design, so the deviations analysis is very important step. In this paper, the aerodynamic parameters estimation methods for lunar-earth high-speed reentry capsule are studied firstly, and the main factors on influencing estimation deviation are analyzed. On this basis, the deviation ranges of main aerodynamic parameters are computed by Monte Carlo method. The results show that the measurement errors of atmospheric parameter, acceleration, attitude angle, altitude, velocity are main factors on influencing estimation deviatons. The deviation ranges of trim angle of attack are very small, and the deviation ranges of lift-drag ratio and aerodynamic coefficients are larger at very high altitude because of the measurement errors of acceleration and atmospheric density. The methods of uncertainty analysis using modified Cramer-Rao to calculate the deviation of pitch moment derivatives and control force are feasible. The results of deviation in this paper can provide the basis for the design and analysis of reentry capsule.