A medical observation system, a control method, and a program are provided, which are capable of easily reducing the possibility that illumination light directly enters an eye by accident. A medical observation system 1 includes: an imaging unit 21 that captures an object and generates an image signal; a light output unit 22 that outputs illumination light in a capturing direction of the imaging unit 21; a determining unit 942 that determines the usage state of the imaging unit 21; and an illumination controller 944 that controls illumination light emitted by the light output unit 22 based on a determination result of the determining unit 942.