Polymer‐based nanohybrid materials were created using sustainable sepiolite clay composed from ubiquitous elements. Although sepiolite is generally recognized as a fibrous natural clay mineral, it turned out to be an acicular microcrystal because of the organo‐modification of the outermost surface. Surface modification was performed using phosphonic acid derivatives containing hydrocarbon chains or fluorocarbon chains. Formation of a bidentate bond enhanced the desorption temperature and made nanocomposite preparation possible by melt compounding with polymers having a high melting point. As a result of organo‐modification, amphiphilic sepiolite was obtained, and nanodispersion in an organic solvent was achieved. This technology was useful for detailed evaluation of sepiolite morphology. The nanocomposite of crystalline polymers/organo‐modified sepiolites achieved uniform dispersion of these nanofillers in the matrix polymer. The introduction of 1 wt% nanofillers did not impair the transparency of the matrix polymer. As a result, a lamellae structure of the polymer developed, the crystallinity increased, and the mechanical properties improved. In addition, the crystallization temperature was improved, indicating that organo‐modified sepiolites may act as a nucleating agent. It was found that sepiolite nanofiller with a highly aggregated tendency can achieve a well‐nanodispersed state, even in phase‐separable fluoropolymers, by applying fluorocarbon modification. POLYM. ENG. SCI., 60:541–552, 2020. © 2019 Society of Plastics Engineers