Three-dimensional hierarchical nanocomposites consisting of one-dimensional carbon nanotubes (CNTs) and two-dimensional lamellar flakes (such as clay, layered double hydroxides) show unexpected properties for unique applications. To achieve a well-designed structure with a specific function, the uniform distribution of CNTs into the used matrix is a key issue. Here, it is shown that a hierarchical composite of single/double-walled CNTs interlinked with two-dimensional flakes can be constructed via in-situ CNT growth onto layered double hydroxide (LDH) flakes. Both the wall number and diameter of the CNTs and the composition of the flakes can be easily tuned by changing the proportion of the transition metal in the LDH flakes. Furthermore, a structure with continuously interlinked CNT layers alternating with lamellar flakes is obtained after compression. The hierarchical composite is demonstrated to be an excellent filler for strong polyimide films. This study indicates that LDH is an extraordinary catalyst for the fabrication of hierarchical composites with high-quality single/double-walled CNTs. The as-obtained CNTs/calcined LDHs nanocomposite is a novel structural platform for the design of mechanically robust materials, catalysts, ion-transportation, energy-conversion, and other applications.