The polyelectrolyte multilayer films were prepared by the layer-by-layer deposition of polyelectrolytes on the charged surfaces substrates. A simple process was developed to create a large area and discrete microporous thin films based on PDDA/NaPSS multilayer films by using immersing the multilayer film into pure water at an appropriate temperature and period. The microporous morphology of the multilayer film is controlled by temperature and time, and observed by atomic force microscopy. It is observed that the total area of the micropores in the films increased with immersing temperature and time. In addition, the microporous process of PEM films in hot pure water is discussed. This unique way to fabricate the microporous films has potential applications to the fields from microelectronic materials to biomaterials.