<p>This study proposes innovative control and replica molding techniques for an intelligent polymer micro-structured soft mold with flexible characteristics. It first introduces a geometric structure design method using metamaterials. The soft mold adopts an auxetic geometric configuration that integrates metamaterial properties. This approach incorporates specific injection materials into the geometric structure to achieve control over their mechanical behavior. By managing injection and environmental parameters—and leveraging a detailed understanding of the Poisson’s ratio of the metamaterials—the study facilitates the design and development of soft micro-structured soft molds. A series of studies on the imprint replica molding process were conducted to effectively control the mechanical properties and microstructural variations of the soft mold. Experimental results show that the magnetic-assisted, injection-based intelligent polymer micro-structured soft mold with flexible metamaterials developed in this study demonstrates excellent replication performance in both simulation and experimentation. This process presents an innovative development pathway for microsystem components.</p>