Trajectory parameters (including the position, velocity, and attitude angles of a vehicle) and air data (consisting of the flow angles, the Mach number, and the freestream static pressure) are vital data for the analysis and evaluation process in the hypersonic flight tests. This paper describes a data fusion estimation algorithm for a flush air data sensing system/inertial navigation system/global positioning system integrated system, which is used to estimate the trajectory parameters and air data for an unpowered hypersonic vehicle. In the approach, the raw outputs of flush air data sensing system (i.e. the surface pressure measurements) are integrated with global positioning system results (the vehicle’s position and velocity) and inertial navigation system measurements (including the acceleration and the angular velocity measurements) by using a nonlinear Kalman filter algorithm. Firstly, the system state vector is defined with the trajectory parameters, the biases of the inertial sensors and the winds. Then, the system dynamic models are built based on the motion equations of an unpowered hypersonic vehicle, the inertial sensor error models and the wind model. Besides, the system measurement vector is designed with the global positioning system results and the flush air data sensing system raw outputs. Based on these works, the system state is directly estimated by using the cubature Kalman filter algorithm. After that, the air data is calculated based on the estimated values and a high-fidelity model of atmosphere. Simulation cases are implemented to assess the performance of the proposed algorithm. The results show that the proposed method could estimate the trajectory parameters and air data for hypersonic vehicle with a high precision.