Traditional multiplex real-time polymerase chain reaction (PCR) enables the simultaneous detection of multiple targets by incorporating two or more pairs of specific primers into a single reaction system. However, traditional quantitative PCR remains limited in its multiplexing capability. By utilizing hydrogels combined with specific primers as a carrier for multiplex PCR, it is possible to immobilize multiple primers targeting different sequences. Furthermore, hydrogels binding distinct primers can be differentiated via hydrogel encoding, array chips, or patterning technologies, thereby facilitating real-time, rapid detection of multiple samples. Characterized by water content, good biocompatibility, and tunable three-dimensional crosslinking networks, hydrogels allow for precise control over size through the adjustment of monomer composition and crosslinking methods. This structural design provides appropriate spatial confinement while maintaining aqueous-phase reaction conditions. Notably, regulating the pore structure of hydrogels enhances PCR efficiency, while physical or chemical fixation enables the fabrication of hydrogel array chips. This paper briefly outlines the principles and developmental history of traditional and multiplex PCR, and comprehensively elaborates on the mechanisms, advantages, and research progress of hydrogel-based multiplex PCR. Finally, the prospects and current challenges of hydrogel PCR detection platforms are discussed.