This study reports the application of illite as a clay filler and direct fluorination as an organophilic modification for clays. Illite was also modified using conventional methods, with reagents such as 3-aminopropyltrimethoxysilane and hexadecyl-trimethoxysilane for comparison of the resultant illite/polypropylene (PP) composites with the fluorinated illite/PP composites. The thermal properties, flame retardancy, and mechanical properties of the resultant composites were also investigated. Fluorination of illite resulted in exfoliation and more thermally stable organophilic modification compared with the conventional silane treatment. When comparing two different silane-treated illite/PP composites with fluorinated illite/PP composites, fluorinated illite had better thermal stability and exfoliation after modification and more improved dispersion in PP matrix. This resulted in improved thermal stability, flame retardancy, and mechanical properties compared with the silane-treated illite/PP composites. The fluorinated illite/PP composite exhibited a 28% increase in thermal stability and a 50% increase in flame retardancy compared with neat PP. Fluorination of illite yielded at least 50% further improvement in the thermal stability and flame retardancy of the resulting illite/PP composites compared with the conventional silane treatments.