0D nanomaterials with high efficiency of atom utilization possess extraordinary tunability over bulk materials. Precise reconstruction of atoms in a 0D nanoparticle toward tuning of crystalline phases and defects is highly desirable but remains a grand challenge. In this study, a crystallization rate‐controlled strategy is reported to achieve controllable reconstruction of atoms in situ, which inducts a series of monodisperse 0D molybdenum carbide nanoparticles (Mo x C NP) that anchor on a carbon matrix with adjustable crystalline phases and atom vacancies. Aberration‐corrected transmission electron microscopy, electron paramagnetic resonance technique, density functional theory calculation, and electron holography jointly reveal the atomic reconstruction process and confirm its remarkable effects of optimizing the local electronic states and enhancing the heterointerface interactions. As a result, the optimized MoC/Mo 2C heterostructure on the carbon matrix is shown to enable the promoted dielectric response and generate more than 90% absorption of lower‐frequency microwaves (the current 5 th‐generation communication band). The control of atomic reconstruction may provide an effective pathway for unlocking tunable dielectric properties of 0D nanomaterials toward various technological applications.