Polyamide 66/clay nanocomposites (PA66CN) were prepared via melt compounding method by using a new kind of organophilic clay, which was obtained through co-intercalation of epoxy resin and quaternary ammonium into Na-montmorillorlite. The silicate layers were dispersed homogeneously and nearly exfoliated in polyamide 66 (PA66) matrix. The introduction of silicate layers induced the appearance of the gamma phase in PA66CN at room temperature, more clay loadings would amplify this phenomenon; the addition of clay also changed the structure of the a crystalline phase. The presence of silicate layers increased the crystallization rate and had a strong hetero phase nucleation effect on PA66 matrix. The lower Brill transition temperature of PA66CN can be attributed to the strong interaction between polyamide chains and surfaces of silicate layers.