Multiscale wrinkled structures are widely used in practical applications, such as smart adhesion, surface engineering, and stretchable electronics owing to their easy and low-cost strategy for controlling surface morphologies. This study demonstrates a facile technique for creating multiscale wrinkles of fluorocarbon thin films deposited on soft and stiff polydimethylsiloxane (PDMS) substrates by regulating the elastic properties of the substrates. The elastic properties of the substrates were changed by varying the crosslinking temperatures and the amount of crosslinking agent. The wrinkling structures were strongly influenced by the elastic properties of the substrate during a fluorocarbon polymer sputtering process. For the stiff PDMS substrates, wrinkles with periodic and sinusoidal patterns were observed due to the thermal compression of the bilayer system after deposition. Spontaneous hierarchical structures were generated on soft PDMS substrates by the penetration of fluorocarbon molecules into the PDMS substrates during the sputtering process.