The structural memory effect of layered double hydroxides (LDHs) is one of the important reasons for their extensive use in environmental remediation. In this study, humic acid (HA) was extracted from black soil and sediments and characterized to determine their structures. The regeneration mechanisms of calcinated LDHs (CLDHs) including different divalent metals (Mg-CLDH and Zn-CLDH) in deionized water and different HA solutions were carefully elucidated, and the reasons for the behavior differences in the two materials were explained. The presence of the HAs significantly increased the dissolution rate of Mg2+ ions from Mg-CLDHs and subsequent regeneration of Mg-LDH. Because of the diverse functional groups in the HAs, these groups were complexed with metallic ions such as Mg2+ on the surface of Mg-CLDH in the beginning. During the process, the HAs adsorbed the regenerated LDHs on the surfaces. Therefore, the crystallinity, morphology, and specific surface area of the regenerated Mg-LDH significantly changed, especially the presence of high concentrations of HA. In the case of Zn-CLDH, the regeneration rate of the LDH increased in the presence of HA, but the surface of Zn-CLDH was covered with regenerated Zn-LDH and HA. Then, the inside of the particles could not transform to LDH, leading to poor crystallinity and a significant increase in the ZnO content of the HA system.