The invention relates to a discrete input decoupling device of a six-rotor unmanned aerial vehicle (UAV) and a control system containing the device. The device comprises a coefficient matrix Mco storage module, a structure matrix Mrel storage module, a module which multiplies a coefficient matrix by a structure matrix and stores the product as a mapping matrix Map, a mapping matrix dimension reduction module, a dimension reducing homogeneous linear equation solving module, a basic solution vector normalization module, a differential module, an amplifier gain module, a summation module and a nonlinear resolving module. The device has the following advantage: the all driven six-rotor UAV, a multiple input multiple output system, is decoupled into six single input single output systems, thusrealizing six degrees of freedom independent control of the UAV. The biggest advantages of the device are as follows: after decoupling, the system has simple form and is easy to design control algorithm; the actual rotating speeds of the motors can be quickly calculated by adopting the virtual additional control quantity; and the algorithm has certain robustness toward fluctuation of the rotatingspeeds of the motors.