Three organic ammoniums with different molecular configurations were selected to modify Ca-bentonite and Na-bentonite. The FTIR spectra SEM images and XRD diagrams of bentonite before and after modification were compared. The adsorption performance of bentonite samples for Hg(II) ions was contrasted. The results indicate that the more complex the molecular configuration of organic ammonium, the greater the steric hindrance, and the more difficult it is to insert into the interlayer space. The chelation between the functional groups contained in organic ammonium and the interlayer cations in bentonite is unfavorable for organic ammonium molecules to enter the interlayer space. Some organic ammonium molecules that cannot enter the interlayer space can adhere to the surface of bentonite particles through interaction with functional groups on the particle surface or through electrostatic interactions and hydrogen bonding forces, forming nanocomposites. Thereby, the adsorption performance of benonite samples modified with organic ammonium for Hg(II) ions improved.