The tree was used by archaeologists who were able to decipher the Poneglyphs. As research of the Poneglyphs is forbidden by the World Government, they sent CP9 to attack the archaeologists and called forth a Buster Call. When Spandine, the chief of CP9 back then, activated the Buster Call to destroy Ohara, the tree fell and crushed almost everything. It is here where Nico Robin learned to read this language, that still remained unbeknownst to the other archaeologists. Its library was the oldest known structure in the One Piece world.
Aside from the archaeologists research of the poneglyph located there, the Tree of Knowledge contained thousands of historic resources that were gathered from all across the globe over hundreds of years. After the Tree of Knowledge caught fire during the Buster Call, the archaeologists desperately threw books into a nearby lake and their efforts saved enough books to fill up the entire lake.