Legolas, named after an elf in Lord of the Rings, helped researchers understand how the animals hunt together.
The body was found next to a highway along with a shotgun cartridge, in what Cheetah Conservation Botswana called an "unnecessary and unprovoked attack".
The death is being investigated as a poaching case.
It comes after another famous big cat, Cecil the Lion, was killed in Zimbabwe by a US dentist, sparking worldwide condemnation.
Legolas was not posing a danger to livestock because there were no cattle in the area, indicating the animal had instead been shot in an opportunistic attack, CCB said.
The group said it sympathised with farmers who have problems with predators, but described the killing as "needless and heartbreaking".
At 68.5kg in weight, Legolas was one of the biggest cheetahs ever caught.
He and two of the three other cheetahs he hunted with were fitted with collars that CCB said had "revolutionised" the study of the animals' collaborative hunting techniques, which until then had remained largely unknown.
The killing of Legolas means three of the seven cheetahs fitted with collars for the research project have been shot.
The estimated population of 10,000 wild cheetahs in Africa today is classified as 'vulnerable' in the IUCN's Red List of threatened species.
A Botswanan cheetah called Legolas that was being studied by researchers has been killed, conservationists said.