Temperature dependent Raman spectra of BiB3O6 crystal and its melt were recorded and the microstructure of BiB3O6 melt was predicted. Multiple theoretical methods including quantum chemistry ab initio calculation and DFT (Density Function Theory) methods were applied to simulate the BiB3O6 crystal and melt structure and Raman spectra. It was demonstrated that B—O triangles and Bi lattice in the crystal reveal little affected in structure while B—O tetrahedra shows severe distortion with increasing temperature, especially B—O tetrahedra disappears after being completely melt. The microstructure of BiB3O6 melt consists of six-member ring, ［B6O12］6-, which varies in bond lengths and angles individually. Cation Bi behaves to balance the charge of anion cluster, and the oxygen coordination number of cation Bi is 3, different from the crystal situation in which cation Bi is coordinated with 6 oxygens.