The nanoscale dispersion of rod-like crystal bundles or aggregates of natural palygorskite (PAL) is not only significant in practical application but is also a challenge. In this paper, phytic acid (PA) was introduced during high-pressure homogenization (HPH) process to simultaneously disperse PAL crystal bundles and restrain the re-aggregation of the dispersed nanorods. SEM, TEM, XRD, FTIR and N₂ adsorption–desorption analyses confirmed that the crystal bundles or aggregates of PAL were highly disaggregated and dispersed to individual nanorod with no disruption to the aspect ratio of rods after being homogenized at 30 MPa, and PA molecules are favorable to dispersion and restrain the re-aggregation of nanorods. The nanoscale dispersion of PAL rods increased the BET specific surface area and Zeta potentials, and effectively improved the colloidal properties. The colloidal viscosity of modified PAL was sharply increased by 110.4% (from 1728 mPa·s to 3636 mPa·s) at the optimal dosage of PA (0.1 wt.%) and the homogenization pressure of 30 MPa, and the suspension stability was clearly enhanced by 71%. This simple disaggregation process provides a new industrial approach to produce nanoscale PAL and extend its application in modern industry.