Shale gas exploitation produces a large amount of waste liquid, which cannot be fully recovered and discharged. Discharged wastewater contains several chemicals, including petroleum hydrocarbons, salts, and heavy metals. Amine compounds can absorb harmful gases but may lead to the presence of these compounds in wastewater. Some amine compounds may cause DNA mutations and health threats to humans and animals. Inspired by the assembly of artificial two-dimensional structures, this paper attempts to shape montmorillonite (MMT) with a natural layered structure. Specifically, a functional 2D/3D amine compound collector within the limitations of 2D MMT (Mt) was prepared by self-assembling cyclodextrin molecules. With the assembly of cyclodextrin (CD) molecules, the two-dimensional Mt. layer length increased from 12.14 to 19.11 Å. Adsorption experiments revealed that functional MMT powder (FMP) has good trapping ability for amines, that the adsorption of amine groups on FMP decreases with increasing temperature, and that it has greater potential to remove amine compounds with fewer carbon chains. Through molecular dynamics simulation, it was found that there was a molecular binding energy between FMP and branched polyethyleneimine (BPEI), indicating that FMP had a spontaneous adsorption effect on BPEI. Furthermore, their adsorption favored the Langmuir isotherm model and the pseudo-second-order kinetic model. This study also provides a new collector for the total organic carbon (TOC) advanced treatment system. Compared with that of ozone and UV treatment, the removal rate of FMP is 10 times higher than that of activated carbon and active resin, which can better remove polar molecules and is beneficial for gas field water recovery.