The extensive use of color dyes in modern society has resulted in serious concerns of water contamination. Many organic dyes bear charges; thus, materials of opposite charges have been tested for sorptive removal. However, the results from several studies also showed that anionic dyes methyl orange (MO) and alizarin red S (ARS) could be removed from water using minerals of negative charges, but the mechanisms were not addressed. In this study, negatively charged clinoptilolite was tested for its removal of anionic dyes MO and ARS from water under different physico-chemical conditions and to investigate the mechanism of Mo and ARS removal. The sorption capacities were 166 and 92 mmol/kg for MO and ARS, respectively, confirming the uptake of anionic dyes on negatively charged framework silicates. The influence of solution pH and ionic strength on MO removal was minimal, indicating the strong affinity of anionic dyes for clinoptilolite in comparison to other inorganic species. It was speculated that the N in the dimethyl group may bear a partial positive charge, which may have a net electrostatic attraction to the negatively charged mineral surfaces for MO sorption. For ARS, sorption may involve hydrogen bonding formation between the dye and the clinoptilolite. Moreover, under the experimental conditions, the MO molecules form dimers in solution via dimeric π-π interactions. Thus, the sorption of the dimers or aggregation of the MO monomers and dimers on clinoptilolite surface was attributed to additional MO removal, as suggested by molecular dynamic simulations. The speculation was supported by FTIR analyses and molecular dynamic simulations. As such, negatively charged Earth materials may be used as sorbents for the removal of certain anionic dyes via sorption, a new perspective for the innovative use of Earth materials.