To provide a medical observation system, an apparatus for controlling an endoscope system, and a method for controlling the same.A medical observation system includes a multi-link structure in which a plurality of links is mutually coupled by joint parts, a medical observation apparatus attached on the multi-link structure, a control part configured to control the multi-link structure or the medical observation apparatus, and a user interface part by which a user inputs an instruction to change a visual field of the medical observation apparatus. When a user instructs to move a visual field of the medical observation apparatus vertically or horizontally, to rotate an oblique-viewing endoscope, or to change a magnification of the visual field via the user interface part, the control part controls the multi-link structure or the medical observation apparatus.
