Palygorskite (Pal) was treated with organic acids to explore effects of acid-leaching levels on its structure, shape of rod crystals, color and physico-chemical features. The leaching behavior of octahedral cations of Pal was studied by evaluating the effect of organic acid types, concentration and reaction time. The results show that oxalic acid (OA) has the strongest ability to leach octahedral metal cations in selected organic acids. OA, having acidity, complexing ability and reduction ability, can be attached to the surface of Pal to promote the leaching reaction, and the position at which the reaction occurs is concentrated on the cylinder surface of the rod crystal. The occupied position of metal cations in the octahedral sheets is the key factor in controlling the leaching of Pal. Mg²⁺ ions at the edge of the octahedral sheet prefer to leach out, then gradually deepens into the interior octahedral sheet, and Fe³⁺ and Al³⁺ ions are leached in turn. When the metal cations are almost completely leached, it means that the octahedral sheets are almost eliminated, at this time, the stacked structure is maintained by the deformed tetrahedron. Compared to conventional inorganic acid leaching methods, organic acid leaching does not destroy the shape of the Pal nanorods. Finally, the one-dimensional amorphous silica nanorods with high SiO₂ content of 91.68 wt%, decent rod length, large specific surface area (323 m²/g), high porosity and high whiteness (L* = 86.6, a* = 0.1, b* = 3.2) were obtained by leaching with 1 M OA solution for 120 h, indicating that the non-destructive dissolution of the Pal was achieved.