The intercalation process and microstructural development of polybutadiene rubber (BR)/clay nanocomposites cured with sulfur were systematically investigated with respect to the organic modifier (primary and quaternary ammonium compounds) of the clay. X-ray diffraction spectra were recorded at various stages of processing to obtain information about the intercalation process. The rubberâ€“filler interactions was examined on the basis of the surface free energy, stress-softening effect, and crystallization behavior. A well-ordered intercalated structure was obtained in the primary ammonium modified clay (POMMT) and quaternary ammonium modified clay (QOMMT) filled with BR composite. The BR/Q-OMMT composites showed higher mechanical properties and higher hysteresis under tension and lower crystallization abilities than the BR/P-OMMT composites. The results also show that higher interfacial interactions existed between QOMMT and BR than between P-OMMT and BR.