Thin films of an amorphous polymer, polystyrene (PS), and a crystalline polymer, poly(epsilon-caprolactone) (PCL), blend were prepared by spin coating a toluene solution. Surface chemical compositions of the blend films were measured by X-ray photoelectron spectroscopy (XPS), and the surface and interface topographical changes were followed by atomic force microscopy (AFM). By changing the PS concentration and keeping the PCL concentration of the solution at 1 wt %, a great variety of morphologies were constructed. The results show that the morphology of the blend films can be divided into three regions with increasing PS concentration. In region I, PS island domains are embedded in PCL crystals when the PS concentration is lower than 0.3 wt % and the size of the PS island increases with increasing PS concentration. In region II, holes with different sizes surrounded by a low rim are obtained when the concentration of PS is between 0.35 and 0.5 wt %. After selectively washing the PS domains, we studied the interface morphology of PS/PCL and found that the upper PS-rich layer extended into the bottom PCL layer, forming a trench surrounding the holes. In region III, an enriched two-layer structure with the PS-rich layer on top of the blend films and the PCL-rich crystal layer underneath is obtained when the concentration of PS is higher than 0.5 wt %. Last, the formation mechanism of the different surface and interface morphologies is further discussed in terms of the vertical phase separation to a layered structure, followed by liquid liquid dewetting and crystallization processes during spin coating.