Provided are a medical observation system, a control device, and a control method that are configured to prevent flickering of a portion to be observed of an object to be observed and reduce the size of the device. The medical observation system 1 includes an image sensor 212, a second control unit 94 that causes a light source device 3 to simultaneously emit second visible light and excitation light, and an image processing unit 91 that generates a fluorescence image based on a first pixel value that is output from a pixel in which a first filter is arranged and that is contained in image data and a background image based on a second pixel value that is output from a pixel in which a second filter is arranged.