Relics from the ship, including the carpenter's tools, are also available for fellow archaeologists and scientists to study on the website following lengthy work by scientists at Swansea University in Wales.
The technique is known as photogrammetry, using high-resolution 2D photographs to produce detailed 3D models.
"This digital resource enables researchers around the world to join the project and study virtual 3D reconstructions," said professor Catherine Fletcher.
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"Once fully developed, this technology can be applied to many more historic objects, bringing them to an even wider community of researchers while preventing damage to the original remains and artifacts."
The researchers captured 1,000 images of 10 skulls found on the ship to create navigable online models, which they hope other researchers will analyse to eventually recreate full skeletons of some of the 500 men who perished.
The Mary Rose fought three wars with the French but mysteriously keeled over and sank off Portsmouth on July 19, 1545, while fighting off a French invasion fleet.