High-pressure homogenization could disaggregate the crystal bundles of palygorskite and favor the adsorption of electrolyte ions onto its surface through the produced cavitation, shear, and turbulence forces, and has evident influences on the micromorphologies and properties of clay. In this work, a series of palygorskite samples modified with sodium citrate, sodium benzoate, sodium lactate, sodium acetate, and sodium propionate were obtained under the condition of high-pressure homogenization. The effects of type and concentration of sodium salts organic acids on the microstructure, morphology, surface charge, and physicochemical property of palygorskite were studied through x-ray diffraction (XRD), N₂ adsorption–desorption isotherm, field emission scanning electron microscopy, zeta potential, rotational viscosity, and rheological measurements. XRD results confirmed that the crystal structure of homogenized palygorskite was not changed after introduction of sodium salts organic acids, but the aggregates were effectively disaggregated. Modification of palygorskite with sodium citrate made the surface more negatively charged, and the samples exhibited higher specific surface area and rheological properties. This work provided a method to improve the rheological properties of palygorskite suspension through dispersion of clay in sodium citrate solution followed by homogenization at 30 MPa.