Polymer microspheres have been widely investigated because of their applications in areas such as drug delivery, latex diagnostics, and affinity bioseparators. The effect of annealing on polymer microspheres, however, has been rarely studied. In this work, we demonstrate the morphology transformation of polystyrene (PS) microspheres annealed thermally on poly(methyl methacrylate) (PMMA) films. During the annealing process, the PS microspheres gradually sink into the PMMA films and transform into PS hemispheres, driven by the reduction of the surface and interfacial energies. The effect of the film thicknesses on the morphology transformation is also studied. In addition, porous PMMA films or PS hemispheres can be obtained by removing the PS or the PMMA domains of the polymer composites using cyclohexane or acetic acid, respectively.