In this article, the original ultrathin CP-690550 film with thickness in dozens of nanometers was spin-coated onto the rigid support (i.e., silicon wafer). A bilayer structure was then fabricated by using the hyperthermal hydrogen induced cross-linking (HHIC) method , , ,  and  to generate a stiff surface film in the homogeneous ultrathin polymer films. HHIC is a new approach to induce the cross-linking of polymer materials. Studies showed that HHIC is efficient in hydrogen-contained systems. It can induce the cross-linking of various polymer films by selectively breaking CH bonds without the breakage of other chemical bonds  and . Computer simulations and experiments also demonstrated that the cross-linking depth induced by HHIC can be as far as 11 nm for an amorphous polymer film in the premise of maintaining the functional groups of the precursor ,  and . Owing to the great applicability and mildness of HHIC, this process for the preparation of a bilayer structure is potential to be applied in almost all polymer films with nano-scale thickness. After the treatment of HHIC, the bilayer was heated above the glass transition temperature of the polymer and then annealed for a selected time. Upon cooling, the film wrinkled into sophisticated patterns with nano-scale wavelength (λ = 150–300 nm). Meanwhile, the morphology of wrinkles gradually changed between the convex bumps and the labyrinth. By regulating the processing parameters, it was found that the wavelength and the morphology of wrinkles were influenced by the thickness of the original ultrathin film, the HHIC treatment time and the annealing temperature. Three typical polymers (polystyrene (PS), poly(styrene–isoprene–styrene) triblock copolymer (SIS) and crystalline polylactic acid (PLA)) were used to test the applicability of this wrinkle fabrication approach.