In this study on a novel glass‐ceramic containing hexagonal CaAl2Si2O8 crystals embedded in a SiO2–Al2O3–CaO glass, we used molecular dynamics simulations to unravel the toughening mechanism of the partially crystallized composite material. The crystalline phase is composed of alternate layers of SiO4/AlO4 tetrahedra and calcium ions. After careful modeling of crystals embedded in the glass matrix, we conducted crack propagation simulations using single‐notched models. We found that: (a) when a crack propagates parallel to the cleavable calcium layer, the glass‐ceramic breaks in a brittle way since the crack passes through the fragile interlayer promptly, (b) the stiffer SiO4/AlO4 oxide layer can inhibit crack propagation, and the crack is thus deflected to the interface between the crystal and the glass matrix; and (c) a calcium layer present between the glass matrix and the edge of the CaAl2Si2O8 crystal is more fragile than those inside the crystal, indicating that cracks prefer to travel along the glass‐crystal interface. These theoretical simulations successfully demonstrated that the anisotropy and the fragile feature of the crystals lead to microcrack toughening of the glass‐ceramic. In addition, we discuss deformation anisotropy in the microscale by constructing a larger model that includes randomly orientated multiple CaAl2Si2O8 crystals.