The invention discloses a BD/DNS/IMU autonomous integrated navigation system and a method thereof. The system includes an airborne navigation computer, an IMU, a Doppler radar, a BD, an air data system, a data recorder, a monitoring system and an AHRS, wherein the IMU, the Doppler radar, the BD, the air data system, the data recorder, the monitoring system and the AHRS are connected with the airborne navigation computer. The method comprises the steps that a self-adapted Kalman filtering model is established by the adoption of a 'position + speed' matching mode, after pose matrix transformation is performed on the Doppler radar, differential operation is performed on velocity measurement information under the navigation system and velocity information calculated through inertial navigation solutions, and differential operation is performed on the position information outputted by the BD and the position information calculated through inertial navigation solutions; difference values obtained serve as observed quantity to perform Kalman filtering information fusion, and loop iteration is preformed on error variances of all branch systems in a state equation of a filtering estimating system; real-time closed-loop estimation is carried out, and all parametric variables in an inertial navigation system, the Doppler radar and the BD are amended to obtain final integrated navigation results after filtering correction. According to the BD/DNS/IMU autonomous integrated navigation system and the method thereof, long-endurance navigation can be carried out in an airborne and seamless mode in real time, navigation accuracy is high, and cost is low.