The present invention provides a three-degree-of-freedom hybrid vibratory screening mechanism, a control method thereof, and a harvester. The three-degree-of-freedom hybrid vibratory screening mechanism comprises a frame, a vibrating screen, a first driving mechanism, a second driving mechanism, sensors and a controller; parallel drive of hydraulic motors are used for achieving two-degree-of-freedom rotational adjustment of the horizontal attitude angle and inclination angle of the screen surface of the vibrating screen, and the first driving mechanism drives the vibrating screen to reciprocate in one degree of freedom, so as to realize three-degree-of-freedom vibration adjustment of the screen surface; a vibration parameter control model is established by means of theoretical analysis in combination with experiment. In the operating process, the sensors installed at the tail part of the vibrating screen monitor the loss rate and distribution of the grains in real time, and the horizontal attitude angle of the screen surface, inclination angle of the screen surface and vibration frequency are self-adaptively optimized and adjusted to promote uniform and discrete distribution of the material on the screen surface, so that the screening efficiency of the material under a condition of non-uniform material feeding is effectively improved and the loss rate of the grains is decreased.