This paper describes a novel, multilayered hot embossing method for fabricating a microstructure pattern on various polymer substrates. The method involves a multilayered hot embossing process with three polymer substrates (polycarbonate, polymethyl methacrylate, and low-density polyethylene), three pieces of microstructured molds, and graphene-based heaters. Only one hot embossing step is required in which a microstructure pattern is directly fabricated onto the three polymer substrates. The total processing cycle time is less than that of the traditional hot embossing process. In this study, thin graphene-based heaters were fabricated and tested. A facility that integrates graphene-based heating and multilayered hot embossing was designed and implemented. Under the proper processing conditions, a hemispherical microlens array and a microcylinder array pattern were successfully fabricated on the three polymer substrates. Finally, the uniformity of embossing temperature and the replication quality of the microstructure patterns were measured and analyzed. The technique shows great potential for the rapid and flexible fabrication of microstructure patterns on various polymer substrates.