Traditional glass molding involves infrared heating; however, the thermal cycle time is long. A molding technique based on three-dimensional carbide-bonded graphene (CBG) has been developed to mold boron silicon glass. This CBG coating on a wafer silicon die can serve as a thin-film resistance heater to heat up the sample surface very rapidly with a relatively low applied voltage. To improve the precision temperature control in hot embossing so as to enhance the process quality, a heating system with lower energy consumption, shorter cycle time, and much more precision control is proposed. We have used COMSOL to simulate the whole heating process, and the heating behavior of a CBG-coated silicon wafer was experimentally investigated. The results showed that the repeatability of the heating system is stable, and it is suitable for precision glass hot embossing. Finally, an example of a precisely fabricated microlens array (Schott P-SK57) is embossed by using this novel heating system.