A novel Hex-Rotor aircraft was proposed to overcome the effect of under-actuation and strong coupling characteristics on the flight performance of existing multi-rotor aircrafts. Based on the unique configuration of six driving rotors, the Hex-Rotor aircraft has the ability to control the space 6-DOF channels independently . First, the structures and characteristics of the Hex-Rotor aircraft were introduced and its dynamic model was established. Then, an autonomous flight control system with a parallel double-loop structure was designed, in which the command-filter backstepping approach was introduced into the attitude stability augmentation control loop, and the translational controller based on the active disturbance rejection control technique was used in the position loop. Finally, the total independent control of the aircraft on 6-DOF channels was achieved in the numerical simulation and the influences of unknown external disturbances and model uncertainties on the flight control performance were overcome. The prototype experiment results indicate that the horizontal tracking errors, altitude errors and attitude errors for the aircraft are limited in ±4 m, ±3 m, and ±005 rad, respectively, which are all according with the precision ranges of measurement units and mean that the prototype has tracked the reference translational and attitude commands accurately. The simulation and experimental results verify that the designed Hex-Rotor aircraft has desired maneuvering capability, and the control system is able to guarantee the autonomous tracking flight of the aircraft.