The CaO–B2O3–SiO2(CBS) glass-ceramics with low sintering temperature and good microwave dielectric properties have been applied on the famous commercial low temperature co-fired ceramics (LTCC) Tape for passivation substrate materials for 5G/6G technology. However, the phase separation and its relationship with the crystallization is rarely studied but extremely important for understanding and designing the high-performance CBS glass-ceramics. Herein, we find that the phase separation type of CBS glass-ceramics changes from metastable immiscibility to stable immiscibility with the increase of B2O3 content. In the metastable immiscible glass-ceramics, three phases are observed, including continuous borate-rich and silicate-rich phases as well as spherical silicate-rich phases. In the stable immiscible glass-ceramics, the silicate-rich phases transform into petal-liked shapes. β-CaSiO3 nuclei are formed in fractions with BO3/SiO4 equaling to 0.56. Notably the β-CaSiO3 nucleus do not grow after heat treatment at 850 °C, but grow at higher temperatures. Phase separation hinders the precipitation of β-CaSiO3 and promoted the formation of CaB2O4 and SiO2. In addition, interfacial defects caused by phase separation alter the crystal barrier and promote the formation of α-CaSiO3. However, α-CaSiO3 dissolves at 1000 °C and may provide Ca2+ cations together with the borate-rich phase for the regrowth of β-CaSiO3. Our work provides another perspective for understanding the effects of phase separation on crystallization in CBS glass-ceramics, contributing to improving the microwave dielectric performance by structural design.