In the present work, Mg₂Al-layered double hydroxide (LDH) intercalated with cubane-1,4-dicarboxylate anions was prepared from the reaction of solutions of Mg(II) and Al(III) nitrate salts with an alkaline solution of cubane-1,4-dicarboxylic acid by using the coprecipitation method. The successful preparation of a nanohybrid of cubane-1,4-dicarboxylate(cubane-dc) anions with LDH was confirmed by powder X-ray diffraction, FTIR spectroscopy and thermal gravimetric analysis (TGA). The increase in the basal spacing of LDHs from 8.67 Å to 13.40 Å shows that cubane-dc anions were successfully incorporated into the interlayer space. Thermogravimetric analyses confirm that the thermal stability of the intercalated cubane-dc anions is greater than that of the pure form before intercalation because of host–guest interactions involving hydrogen bonds. The interlayer structure, hydrogen bonding, and subsequent distension of LDH compounds containing cubane-dc anions were shown by molecular simulation. The RDF (radial distribution function), mean square displacement (MSD), and self-diffusion coefficient were calculated using the trajectory files on the basis of molecular dynamics (MD) simulations, and the results indicated that the cubane-dc anions were more stable when intercalated into the LDH layers. A good agreement was obtained between calculated and measured X-ray diffraction patterns and between experimental and calculated basal spacings.