Hughes will lead the Kew diploma, which has run since 1963 and has trained Alan Titchmarsh, Alys Fowler, Dan Pearson and Matt Biggs.
Kew horticulture director Richard Barley said: "This is a very exciting chapter for Kew's school of horticulture. Our investment in future generations of horticulturalists is essential to meet the needs for professional and practical skills in the field."
A Kew representative said the role differs from the previous principal of the school of horticulture because it "incorporates strategic and developmental responsibilities."
The RHS will begin to look for a successor for Hughes next week.
Martin Staniforth has been acting principal of Kew's horticulture school after Emma Fox left in 2012.