A new polymorphism of Ba3W2O9 is discovered with the use of a high-pressure synthesis technique and its crystal structure is determined by single-crystal X-ray diffraction and transmission electron microscopy. The crystal structure was isostructural with that of Ba3Re2O9, having a hexagonal unit cell of R (3) over barm symmetry with a = 0.574060(10) nm and c = 2.08256(4) nm. The high-pressure (HP) phase is obtained from a transformation of an ambient-pressure (AP) phase of the compound, which has the Cs3Tl2Cl9-type structure. The most notable change in the transformation is the connection of WO6 octahedra. The HP phase has corner sharing octahedra, which form a bilayer structure, while the AP phase has face-sharing octahedra of isolated [W2O9] dimers. This type of the structural phase transition is unreported although it is possibly that a sequence of high-pressure structural transformations occurs for similar chemical compositions. The HP phase has W ions in WO6 octahedra with an unusual off-center displacement; although the displacement is slightly relaxed compared with that of the AP phase. The off-center displacement suggests strong hybridization between the W 5d orbitals and O 2p orbitals.