Layered double hydroxides (LDHs) are a typical class of anionic clay minerals whose structural memory effect has been widely used in pollutant adsorption. However, the influencing mechanism of humic acid (HA) on the structural memory effect in adsorption is not clear. In this study, HA was extracted from black soil and sediments, and its effect on the structural memory effect of LDHs with different divalent metals was evaluated in adsorption. Borate complexed with HAs and HAs promoted the dissolution of magnesiumcalcined LDHs (Mg-CLDH), which enhanced their adsorption rate by Mg-CLDH. However, the adsorbed HA caused a decline in the crystallinity of the regenerated Mg-LDH and an incomplete structural transformation, thereby resulting in decreased adsorption capacity. After the complexation of HAs with borate, the resulting compound was adsorbed on the surface of Zn-CLDH. The adsorption rate of borate was effectively improved in the initial stage, but at the same time slowed down the hydration and structural regeneration of Zn-CLDH. Meanwhile, the surface-adsorbed HAs also prevented borate from entering the newly formed layer inside the particles and led to a significant decrease in adsorption performance. When Ca-CLDH was used to adsorb borate, the process mainly occurred through the formation of ettringite. However, the presence of HAs enhanced the stability of the restructured LDHs and hindered the dissolution of Ca-CLDH and the reaction with B(OH) 4− to form ettringite during the regeneration process, which severely inhibited the sorption of borate.