Abstract: Traditional experimental methods are insufficient in the study of layered double hydroxides (LDHs) supramolecular structure and hydration expansion performance, and information on interlayer anionic arrangement and structural water molecules cannot be obtained. Aspartic acid intercalated magnesium aluminum hydrotalcite was synthesized using coprecipitation and ion exchange. The structure of hydrotalcite precursor and its aspartic acid composite materials was characterized by X-ray powder diffraction, differential thermal analysis, and infrared spectroscopy, and Materials Studio software was used to simulate the molecular dynamics of microstructure and hydration properties of LDHs intercalated with the aspartic acid drug. The prepared composite material had a regular layered structure and a single crystal phase. After intercalation with aspartic acid, the interlayer spacing increased from 0.84 nm to 1.13−1.17 nm; after intercalation, the thermal decomposition temperature of aspartic acid increased from 249 °C to 334 °C, greatly improving its thermal stability. The interlayer spacing of the intercalated hydrotalcite obtained from the experiment was close to the molecular dynamics simulation results when N_w=3−4. As more water molecules were inserted between the layers, the greater the interlayer distance became. Hydration energy increased gradually and tended to a certain value. The total number of hydrogen bonds increased gradually, the hydrogen bonds between laminates and anions decreased gradually, but the hydrogen bonds between laminates and water molecules increased gradually. The simulation results are close to the experimental results, which can lay a foundation for the design and synthesis of LDHs-based drug composites.