Poly(3,4-ethylenedioxythiophene)/poly(styrenesulfonate) (PEDOT/PSS) is a widely used conductive polymer in the field of flexible electronics. The ways its microstructure changes over a broad range of temperatures remain unclear. This paper describes microstructure changes at different temperatures and correlates the microstructure with its physical properties (mechanical and electrical). We used High-Angle Annular Dark-Field Scanning Electron Microscopy (HAADF-STEM) combined with electron energy loss spectroscopy (EELS) to determine the morphology and elemental atomic ratio of the film at different temperatures. These results together with the Atomic Force Microscopy (AFM) analysis provide the foundation for a model of how the temperature affects the microstructure of PEDOT/PSS. Moreover, dynamic mechanical analysis (DMA) and electrical characterization were performed to analyze the microstructure and physical property correlations.