Instabilities in systems of a stiff film attached to a soft underlayer lead to the spontaneous formation of surface wrinkling patterns with a high degree of regularity. In the past few decades, surface wrinkling has drawn much attention for its interesting forming process and a wide range of nanoscale applications in getting complex and ordered topologies, fabricating variety of controllable functional materials, and measuring mechanical properties of thin films. Nevertheless, up to now it still remains a great challenge to build up an efficient and simple method to prepare wrinkling patterns at nano-scale for ultrathin polymer films. In this work, hyperthermal hydrogen induced cross-linking (HHIC) method was first employed to create bilayers within ultrathin polymer films, then these bilayers were annealed at high temperature for a certain time before being quenched to room temperature. In this way, delicate wrinkling patterns with wavelength between 150 and 300 nm were prepared for the first time, which were induced by thermal expansion on the ultrathin polymer films. The formation of wrinkling patterns was systematically investigated as function of film thickness, HHIC exposure time, annealing temperature and chemical structure of polymer. Furthermore, by using nano-patterned silicon wafers as templates, well ordered wrinkling patterns can be obtained. Our work provides a new approach for the preparation of wrinkling patterns at nano-scale on ultrathin polymer films, which may be used in the field of nano-fabrication, biological chip, and microfluidics technology and so on.