<p>With miniaturization and thin-film development of multilayer ceramic capacitors (MLCCs), their operating field strength approaches the critical breakdown field strength. Due to the non-homogeneous structure inside the capacitor, the localized electric field concentration can induce local breakdown and insulation failure, which has become a bottleneck in improving its energy storage performance and reliability. In this paper, a mesoscopic to-macroscopic scale phase-field modeling of dielectric breakdown is constructed, and simulations are carried out to investigate the influence of non-homogeneous factors; such as ceramic grain size, crystallinity, and electrode spacing; on their local electric field distributions, breakdown behaviors, and energy storage densities. It was found that high crystallinity enhances polarizability, but also exacerbates inhomogeneity, thereby leading to local breakdown and reducing energy storage density. Moderate heat treatment increases grain size, reduces grain boundary defects, and enhances breakdown field strength and energy storage density. However, excessive grain growth introduces new defects, resulting in the opposite effect. As MLCCs develop in the direction of thin films, the electrode spacing is also reduced; Although this reduces the breakdown field strength, it can enhance the energy storage density by utilizing the multilayer structure. In this paper, the dielectric field breakdown model is combined with phase transition microstructure simulation to reveal the influence of microstructure on energy storage performance, which provides theoretical support and technical path for MLCC performance optimization.</p>