Three-dimensional (3D) Y2WO6 and Y2WO6: Ln3+ microspheres with novel controllable morphology have been obtained by the hierarchical self-assemblyvia a hydrothermal synthesis route with a subsequent heat treatment. The amount of citric acid and polyvinylpyrrolidone (PVP) play crucial roles in the controlling of the morphologies. Hollow, core/shell as well as waxberry-shape Y2WO6 microspheres can be prepared in different reaction systems under the same facile hydrothermal conditions. Metastable phases of the samples form when they are crystallized at low temperature, which transfer to the thermodynamically stable counterpart above 1100 °C. This phase transformation is irreversible. The mechanism of reaction and self-assembly evolution process are proposed. The as-prepared Y2WO6:Ln3+ (Ln = Eu, Er, Sm, and Dy) samples show strong multi-color visible light emission under ultraviolet-visible light excitation. Compared with the monoclinic one, this metastable Y2WO6: Eu3+ phase exhibits different luminescent properties. Due to multi-color luminescent properties, these Ln3+-doped (Ln = Eu, Er, Sm, and Dy) metastable Y2WO6 morophologies controllable microspherical samples may be promising for further fundamental research and find applications in color displays.