Since it was lifted, the ship - housed in a special building in Portsmouth - has been constantly sprayed with chilled water to prevent decay.
But now, scientists from the Mary Rose Trust have decided to switch off the water and launch the main phase of a long-term conservation programme in which the ship's timbers will be impregnated with a preservative chemical for at least 15 years and will then be bombarded with dry air for a further six years.
The chemical - polyethylene glycol - will replace the water within the cells of the timber so that as the ship dries out, the cells do not collapse and cause the timbers to shrink and disintegrate. It is the most sophisticated marine archaeology conservation project undertaken.
Built in 1509, the vessel - then one of the world's largest - sank a mile south-east of Portsmouth harbour in 1545 and lay buried in mud for 447 years before being excavated and raised in 1982. Almost half the vessel had survived intact under the seabed.
Although the ship itself has been raised, further archaeological discoveries are constantly being made. Every year archaeologists dive on to the area of the seabed from which the ship was lifted, in the hope of finding more material.
In May archaeologists plan to carry out a fresh sonar survey of the seabed. The archaeologists hope one day to discover the Mary Rose's longboat - a 30ft rowing boat that the ship towed.
The finds, brought up every year from the sea bed, are usually hidden within chunks of corrosion material known as concretions - and about 15 of these are now examined annually. Each yields about eight artefacts - or the voids left by them. If all that is left is a hole, scientists inject rubber into the void to make a cast of the lost object.
When built the Mary Rose consisted of about 10,000 timbers, of which 4,252 survived and have been lifted. The starboard half of the ship's hull, 1,457 timbers, was raised from the seabed in its entirety, while the 2,895 internal timbers, forming decks and cabins, were lifted separately.
Every internal timber was numbered by underwater archaeologists before being lifted, and - mainly over the past three years - these have been re-inserted into the hull, thus enabling the internal structure to be recreated. A further 425 architectural timbers are also being conserved and will eventually be inserted.
The ship was built in Portsmouth on the orders of Henry VIII and was named after his younger sister. She took part in two naval campaigns against France in 1513. In 1545, after being incompetently manoeuvred, she capsized and sank in front of Henry VIII, who was watching from a castle a mile away.
Archaeologists started their search for the Mary Rose in 1965. After two years the wreck was located with sonar equipment. By 1971, the first timbers were exposed and a full excavation was carried out between 1979 and 1982. The Mary Rose was moved to dry land in October 1982.
The wreck has yielded more than 1,000 pieces of clothing, 7,000 items of weaponry, 29 items of navigation equipment including the earliest steering compass, 46 pieces of medical equipment, 11 musical instruments, 16 writing utensils, 29 items of fishing equipment, much cooking equipment, carpentry tools, gambling equipment and 13 rosaries.
By analysing how these finds were distributed, archaeologists have been able to identify cabins used by the barber-surgeon, the carpenter, the cook and the pilot.
The Mary Rose sank with about 700 people on board, of whom 30 survived. Archaeologists have recovered 200 skeletons.
So far the wreck has cost pounds 15m to excavate, lift, treat and display, and has been visited by three million people. Visitors will be able to see the new conservation work being carried out.
The Mary Rose is on view every day from 10am to 5pm.