To design and prepare novel metal oxide-carbon composites are always considered as a feasible way to explore potential candidates for high-performance electrode materials. In this work, we fabricated the unique composites of MnO nanoparticles and graphene-like carbon flakes by pyrolysis of an inorganic-organic layered compound. As precursors, the inorganic-organic layered compounds create a special two-dimensional space, which induces a novel hybrid of MnO nanoparticles and carbon flakes. The as-obtained ultrathin carbon flakes are not smooth but contain numerous caves, where the MnO nanoparticles are located with the even size of 20 nm. This unique compositing pattern of MnO particles and carbons endows the MnO/CS with a larger contact area and a closer combination between active materials and conductive scaffolds, leading to an excellent electrochemical performance as the anode materials of lithium-ion batteries.