The effect of surface modification of Palygorskite (Pal) on the morphology and the mechanical and thermal properties of Nylon 6/Palygorskite nanocomposites, prepared by melt compounding, was investigated. A Pal mineral was purified, characterized, and surface modified separately with 3‐Aminopropyl trimethoxysilane and tributylhexadecyl‐phosphonium bromide in order to produce polymer nanoreinforcements. Organo‐Pals were characterized through SEM/EDX, FTIR, TGA, and XPS; surface energy was also determined. Experimental evidence confirmed the grafting of surface agents on the Pal surface; as expected, organo‐Pals exhibited high thermal stability and lower surface energy. Nylon 6/clay nanocomposites were melt‐compounded with different Pals at low Pal loadings. Pal dispersion was assessed by SEM and the thermal and mechanical properties were determined. In general, Pal exhibiting lower surface energy produced Nylon 6/Pal nanocomposites with improved Pal dispersion and properties. Pal particles favored the formation of γ crystalline form and increased the decomposition temperature of Nylon 6. The Pal aspect ratio in the Nylon 6/Pal nanocomposites was estimated from the experimental values of the elastic modulus using the Halpin–Tsai model; in addition, the Pal‐Nylon 6 interactions were estimated from the experimental values of the yield strength of nanocomposites with the Pukanszky's model. POLYM. COMPOS., 39:E1531–E1543, 2018. © 2017 Society of Plastics Engineers