Neutron diffraction and Scanning Electron Microscope (SEM) were employed to study complex two-phase coexistence structure and surface morphology of CaO-Al2O3-SiO2(ZnO-BaO-Na2O) glass ceramics prepared under different cooling conditions. With the rapid cooling temperature decreasing from above 850°C to 750°C and 300°C, the length of the needle-like precipitated β-wollastonite crystal decreased from 30 μm to 15 μm and 5 μm, respectively. Meanwhile, the transgranular fracture appeared and the grain boundary became indistinct in the sample rapidly cooled to 750°C, and the microcracks appeared in the samples rapidly cooled to 300°C and below. These phenomena contribute to the decrease of bending strength for the rapid cooling. Neutron diffraction revealed that the unit cell of precipitated β-wollastonite crystal elongated along its three axes and its volume increased at different cooling conditions. With the decrease of the cooling temperature, the elongation of axes and increase of volume were enhanced, implying that the tensile stress of the β-wollastonite crystal increased. At the same time, intensity of the crystal diffraction peaks increased and atomic temperature factors decreased, which revealed that defects inside a smaller size of crystal granular were less than that in larger one. Amorphous peaks at low diffraction angle did not changed with cooling temperature, showing that the middle-range-order inside residual glass phases were almost the same for all cooling conditions, while intensity of amorphous peaks at high diffraction angle increased notably for samples rapidly cooled to below 850°C, showing that rapid cooling may result in severe short-range-order in residual glass phase, which induced tensile stress of crystalline phase from around amorphous phase and therefore lead to occurrence of transgranular fracture and microcracks. This study suggests that rapid cooling to below 850°C should be avoided in order to obtain preferable mechanical properties for CaO-Al2O3-SiO2(ZnO-BaO-Na2O) glass ceramics.