The current study investigates the development of a replica molding process for hypervariable microstructures. Initially, the mold deformation theory for these hypervariable microstructures was derived. Based on this theory, a metal material with magnetic properties was selected as the structural material to create a negative Poisson’s ratio (NPR) geometric structure. The experimental results, obtained by fabricating the NPR geometric mold layer with a metal material with adjustable magnetic properties and controlling microstructure deformation indirectly, validate the deformation theory and its predictions. These results demonstrate that the developed molding process, integrated with the magnetic NPR regulation system, exhibits excellent stability and replication capability. In this study, at the zero height (z = 0) position on the interface between the NPR geometric structure layer and the Polydimethylsiloxane (PDMS), the variation becomes more pronounced with increasing distance from the center of the microstructure. Furthermore, the tendency of the function curve varies accordingly. The primary cause is the lack of constraints on the free ends of both sides and the excessive constraints on the intermediate parts. Under the conditions in this study, the maximum ratio of its influence on the radial diameter thickness was 2.1%. This innovative process facilitates the rapid imprinting of microstructural components and offers the advantage of efficient molding.