Barium strontium titanate (BST) glass-ceramics were fabricated via controlled crystallization with different crystallization routes. Effects of the microwave crystallization and microwave treatment on the microstructure and energy storage properties of the glass-ceramics were systematically investigated. Results showed that microwave crystallization can increase the dielectric constant. In addition, it was found that the microwave process had little impact on the crystallinity (about 90 wt%), but preferred the crystallization of SrAl4O7. Most importantly, the dielectric breakdown strength (BDS) of the glass ceramics was significantly improved from 561.3 to 791.4 kV/cm by the microwave crystallization. And it can be further enhanced to 900.0 kV/cm by conventional crystallization combined with microwave treatment. The corresponding energy densities of samples derived from the microwave processes were increased to 1.05 and 1.13 J/cm3, respectively, compared with the sample fabricated by the conventional crystallization route (0.47 J/cm3).