An endoscopy apparatus having high degree of motion freedom and the operating method thereof are disclosed. The endoscopy apparatus having high degree of motion freedom includes a multi-stage endoscopy module and a control module. The multi-stage endoscopy module includes at least a first endoscopy unit and a second endoscopy unit. The first endoscopy unit and the second endoscopy unit can provide a first bending and a second bending respectively. The second bending is larger than the first bending. When the multi-stage endoscopy module moves to a region near a target observing position, the control module will control the second endoscopy unit to generate slight deformation to observe a real-time state of the target observing position.
