The structural determination of nanomaterials and their application in energy storage and transfer are of great importance. Herein, a layered zirconomolybdate with a two-dimensional structure was synthesized. Atomic resolution electron microscopy was utilized for direct visualization of the structure that was further confirmed by powder X-ray diffraction and X-ray absorption near-edge structure analyses. The structure of the molecular sheet was stable at a high temperature in an oxidative atmosphere. The electrochemical performance of the material was evaluated with a Li battery composed of the calcined material as a cathode. Li ions were reversibly inserted and extracted between the layers without collapse of the structure of the material. The electrochemical properties of the material were derived from the reversible redox activity of the Mo ions and Zr ions in the material as well as the flexibility of the molecular layer of the material.