The “big cheese” is the person with the authority and responsibility for everything within an organization.
In this case, cheese is an Anglicization of chiz, the Urdu word for thing.
In colonial India, the natives picked up the pre-existing English idiom “the real thing” and made it “the real chiz,” which in turn was carried home by the British where to homeland ears chiz sounded like cheese.
In the United States, the “real cheese” was converted to the “big cheese” to describe the most important person in a group.