Emulsifier-free emulsion polymerization was employed to synthesize polystyrene (PS) microspheres, which were then self-assembled into an ordered periodic structure. A photochromic film was formed by adding polydimethylsiloxane (PDMS) around the self-assembly of PS microspheres on a PDMS substrate. During polymerization, the PS microspheres shrunk depending on the amount of the hydrophilic comonomer, sodium 4-styrenesulfonate (NaSS). Variation in structural color was strongly affected by the size of the PS microspheres. Scanning electron microscopy was used to observe the surface and cross sections of the self-assembled microspheres. Results showed that the order and stacking thickness of microspheres were dependent on the drawing rate of the substrate and suspension concentration. High-transmittance photochromic films could be prepared when the drawing rate was lower than 1 mu m/s and the suspension concentration was 20 wt % PDMS surrounding the vacant space between regularly arranged PS microspheres could not only protect them but also increase the degree of matching between the refractive indices of PS and PDMS. The stability of the reflected structural color increased, and the optical transmittance of the photochromic film approached 95% after PDMS was poured between the PS microspheres. A special pattern could be designed and embedded inside the photochromic film. The PS/PDMS photochromic films can also be applied in decorative painting as well as in security devices, color-changing false nails, and privacy filters.