This paper describes the microstructural transformations of borate glass and barium metaborate crystals induced by femtosecond laser. Such structural transformations were verified by Raman spectroscopy. The borate glass is transformed into low temperature (LT) phase of barium metaborate (BaB2O4) crystals after being irradiated for 10 min by a femtosecond laser. In addition, after 20 min of irradiation, high temperature (HT) phase of BaB2O4 crystals is also produced. Further studies demonstrate that LT phase BaB2O4 crystals are formed in the HT phase BaB2O4 crystals after femtosecond laser irradiation for 10 s.