In this work, nylon 6 (PA6) and cationic dyeable polyester (CDP) modified with benzenesulfonate groups were reactively blended in a twin-screw extruder. The well-mixed CDP/PA6 blends were re-molten and statically kept for various amounts of time. The morphology evolution caused by phase separation was observed by a scanning electron microscope (SEM) and an atomic force microscopy-infrared (AFM-IR) technique. In the absence of shear force, the homogeneously mixed blends were found to separate rapidly into two phases because of the poor miscibility between polyester and polyamide. In the early stage, the dispersed phase was small in size and irregular in shape. With prolongation of the phase separation time, the dispersed phase turned into larger and spherical particles to minimize the interface between phases. The phase separation process typically lasted 2 to 7 min. This means that the effects of phase separation on the morphology of the blends cannot be ignored in injection molding, compression molding, or other processing processes short of shear force. The effects of the ratio between polyester and polyamide, the benzenesulfonate content, and the molecular weight of polymers on phase separation behavior were investigated.