Two-dimensional graphene is easy to aggregate and hard to transfer because of the van der Waals forces between graphene layers. The three-dimensional (3D) graphite-like capsules (GCs) disperse well and exhibit robust structural stability and have a potential for promising applications in energy storage, drug delivery, catalyst substrate, etc. Here, we develop a catalytic chemical vapor deposition route for the synthesis of 3D GCs with unprecedented thickness and morphology control. The theoretical results indicate that the strong chemisorption and charge transfer between ZnO and acetylene allow the layer-by-layer formation of GCs that is later confirmed by the experimental data. The 3D GCs are synthesized with thickness control from three atomic layers to ∼300 atomic layers over various oxides with predesigned shapes of microscale tetrapods, nanospheres, nanorods, nanocubes, etc. In particular, the formation mechanism of GCs is investigated using the ZnO surface as a catalyst through systematically experimental approaches. In addition to the high-quality of 3D GCs, this approach provides an unprecedented facile methodological control of coating/functionalizing carbon over various oxides including ZnO, TiO2, SnO2, BaFe12O19, etc.