Captain Eric "Winkle" Brown was the first person to land a jet on an aircraft carrier and holds the record for the most flight deck landings.
Appointed MBE, OBE and CBE, the test pilot died last year at the age of 97.
The items were bought by The National Museum of the Royal Navy for an undisclosed sum after failing to sell at auction.
Nicknamed "Winkle" - after the small mollusc "periwinkle" because of his height - Capt Brown has the Distinguished Service Cross as well as the Air Force Cross.
Over his career, he flew 2,407 aircraft carrier landings and 487 different types of aircraft.
The collection also includes Capt Brown's Air Force Cross, awarded in 1947, and the Defence Medal with King's Commendation for Brave Conduct.
David Morris, from The Fleet Air Arm Museum in Yeovilton, said the test pilot had flown everything from captured German and Italian aircraft to "British experimental aircraft".
"He flew an amazing amount of aircraft - 487 types - which is a record , which is unlikely to be beaten," he said.
"For all of his flying career the part that meant most to Eric was Navy flying, so for them [his medals and log books] to be here in our collection would have pleased him immensely."
Medals and log books belonging to the Royal Navy's most decorated pilot have been unveiled at a Somerset museum.