The preparation of hierarchical nanoporous films is of great significance for their potential applications, but the development of a facile method to synthesize such films method remains a great challenge. In the current work, hierarchically honeycomb-patterned polydimethylsiloxane (PDMS) films with unique nanostructures were synthesized by simply depositing an acid solution, specifically consisting of a mixture of H2SO4, HNO3, and DI water, on PDMS films displaying regular concave structures. During the post-processing, secondary extrusions were generated on the surfaces of such PDMS films, leading to the formation of highly hierarchical honeycomb-shaped patterns. In the synthesis, the composition of the acid solution played a critical role in the formation and growth of the secondary extrusions. The morphological evolution of the PDMS films during the post-processing proceeded along different pathways depending on the experimental conditions of the process. Based on our results and observations, a plausible mechanism explaining the formation of the hierarchical honeycomb-shaped patterns and the morphological evolution during the synthesis was proposed. The developed approach provides a simple route for fabricating polymer films with unique hierarchical honeycomb-shaped patterns and without the need for any expensive or sophisticated lithographic patterning instruments.