A high repetition rate femtosecond laser is used to irradiate the surface of dysprosium molybdate glass, and then two kinds of crystals, the β′-Dy2(MoO4)3 crystal with MoO4 structure cell and the α-MoO3 crystal with MoO6 structure cell, could be identified in the modified regions through micro-Raman spectra analysis. Energy dispersive spectra (EDS) further show that concentration of Mo element would be reduced in the center of the irradiated region as well as the α-MoO3 crystallization region, which indicates that laser induced microexplosion causes a rarefaction center under high temperature and pressure shockwave. With the irradiation time increasing, a phase transformation from β′-Dy2(MoO4)3 to α-MoO3 occurs. It implies that the concentraion reducing of Mo element due to femtosecond laser continuously irradiating could effectively promote the transformation of Mo-O structure from MoO4 to MoO6, and further for the α-MoO3 crystallization in lower Mo elements region.