Nylon 6 (PA6)/clay hybrids have been prepared using a direct melt intercalation technique by two processes. One is PA6 melt-mixing with modified clay, the other is PA6 melt-mixing with natural (Na+ base) clay using an ammonium salt bearing long alkyl chains as a polymer/clay reactive compatibilizer. Their structure and flammability properties are characterized by X-ray diffraction, transmission electron microscopy and cone calorimeter experiments. The results of the cone calorimeter experiments show that hybrids made by these two processes have a lower heat release rate peak and higher thermal stability than that of original PA6. Meanwhile, X-ray diffraction was used to investigate PA6/clay hybrids with various cooling histories from the melt, including medium-rate cooling (air cooling) and rapid cooling (water-quenched). In contrast to pure PA6 dominated by the α phase, the addition of clay silicate layers by these two methods favors the formation of the γ crystalline phase in PA6/clay hybrids. Flammability and phase-transition studies confirm that silicate layers added by these two methods have a similar nanoeffect and nanodispersion in the PA6 matrix.