In this study, we develop a novel high-throughput micronanopatterning system that can implement continuous mechanical pattern inscribing on flexible substrates using a rigid grating mold edge. We perform a conceptual design of the process principle, specific modeling, and buildup of a real system prototype. This research also carefully addresses several important issues related to processing and controlling, including precision motion, alignment, heating, and sensing to enable a successful micronanopatterning in a continuous and high-speed fashion. Various micronanopatterns with the desired profiles can be created by tuning the mold shape, temperature, force, and substrate material toward many potential applications involving electronics, photonics, displays, light sources, and sensors, which typically require a large-area and flexible configurations.