Palygorskite is a natural nanorod with about 20–70nm in diameter and 1–2μm in length, but the intrinsic existence form of palygorskite as aggregates or bundles effaces its nanometer characteristic. In this work, a novel method for effective disaggregation of crystal bundles of palygorskite was developed via freezing assisted extrusion and homogenization process. The effects of freezing process and freezing time on the disaggregation state, micro-structure and properties of treated palygorskite were studied using scanning electron microscopy (SEM), transmission electron microscopy (TEM), infrared spectroscopy (IR), X-ray diffraction (XRD), N2 adsorption–desorption isotherm (BET), and rotary viscosity measurements. The dispersion of palygorskite depended greatly on freezing time, and a highly dispersed palygorskite nanorods were achieved after freezing for 4h followed by homogenization at 10MPa. The treated palygorskite retained its original structure, and the rods were rarely disrupted. The specific surface area of palygorskite enhanced from 163m2/g to 237m2/g as the freezing time increased from 0 to 8h, and the rotary viscosity increased from 152mPa·s of natural palygorskite to 2682mPa·s, which was about 2.0 folds of the sample without freezing treatment.