Palygorskite (Pal), as a valuable naturally available one-dimensional (1D) nanomaterial, has received greater attention in both academic and industrial areas. However, the rod crystals of Pal are usually existed as crystal bundles or aggregates in natural Pal owing to the stronger hydrogen-bonding and Van der Waals' interaction among rods, which limit the dispersion of Pal into water or other medium. Thus, the unique nanometer characteristics of Pal cannot be fully developed and its extensive application was limited, and so the high-efficient disaggregation of Pal aggregates into individual nanorods becomes a key to utilize the nanometer properties and develop the related product. In this review, the scattered information on the dispersion of crystal bundles or aggregates of natural Pal for application in nanocomposites was organized, and the high-pressure homogenization technology and integration disaggregation process proposed by our groups were especially introduced. The crystal bundles could be disaggregated by the "shearing, impact and cavitation" effects generated during high pressure homogenization process, without damaging the crystal structure and length of nanorods. The resultant nanoscale rods of Pal exhibit remarkable improvement of the colloidal, adsorptive, mechanical, thermal, and surface properties. These results reflect a scientific technical contribution to the nanocrystallization of the aggregated Pal rod crystals and its key role to develop various functional nanocomposites.