Abstract: Performing aerodynamic measurement can acquire a mounts of data during Mars entry exploration. This work benefits for aerodynamic characteristics confirmation and improves key flight performance, such as landing accuracy. In this study, an aerodynamic measurement system scheme is proposed based on trajectory reconstruction and flush air data system. Angle of attack and angle of side slip are measured by output error method with measured trajectory; dynamical pressure is measured via Flush air data system and least square optimal estimation. By simulation, it shows that the proposed measurement scheme has high measure accuracy, and dynamical pressure accuracy is 1%, and angle of attack and angle of side slip accuracy are improved more than one time. This study is helpful for aerodynamic measurement of deep-space exploration entry flight, such as Mars exploration entry flight.