The structural transformation of layered double hydroxides (LDHs) plays an important role in a variety of natural environmental behaviors. As one of the important ways of structure transformation in LDHs, the structure memory effect closely interacted with humic acid (HA). However, the role of functional groups in HA is unclear because its structure is relatively complex. Therefore, seven representative small molecules of single or double aromatic compounds were selected to explore their influence on the regeneration of different LDHs, thereby revealing key function groups in HA. As a result, ortho-benzene compounds could more effectively affect the regeneration of LDHs than other model compounds. For these compounds, the aliphatic chain length and aromatic ring size have little effect on regeneration of LDHs. However, increasing the number of carboxyl or hydroxyl groups affected the results, although all of them accelerated the regeneration rate of LDHs. Additionally, LDHs during the regeneration have a positive adsorption effect on both o-carboxyl and o-hydroxyl aromatic compounds; however, they have shown different effects on the regeneration of LDHs. Phthalic acid revealed no effect on the structure and crystallinity of regenerated LDH, while catechol inhibited the regeneration process and decreased the crystallinity of regenerated LDHs. The effects of o-hydroxyl aromatic compounds, such as catechol, are also dependent upon the type of LDHs. They have an inhibitory effect on the crystallinity of the regenerated Mg−LDH within a short time or with a high concentration but have no effect on its morphology. Although o-hydroxyl aromatic compounds have no effect on the crystallinity of regenerated Ca−LDH, the crystal growth was suppressed. This is due to the difference in the regeneration processes between two LDHs. These results provide a more detailed theoretical basis for understanding the influence of HA on the structural transformation of LDHs or even other minerals, such as hydroxides, in the environment.