Although PCR is a typical temperature-variable amplification technique for nucleic acids, it still faces challenges in rapid screening, such as low speed, poor sensitivity, inferior visualization, and weak stability. In this paper, a universal functional nucleic acid (FNA) lateral flow magnetic biosensor was constructed using blocking super PCR (BS-PCR) and a magnetic test strip (MTS). In theory, the visualized and magnetic output of dsDNA-based amplicons were achieved via ssDNA/dsDNA conversion by blocking linkers in the PCR primers and magnetic probes. In application, high-speed, super-sensitive, highly stable rapid screening was realized by taking advantage of the speediness of the super PCR reactor and the anti-background interference, visualization and high stability of magnetic signal readout. The genetically modified maize MON810 was selected as a double-stranded model target, while 5-min BS-PCR and 5-min magnetic signal readouts achieved the screening results within 10 min. Furthermore, the exponential PCR amplification and magnetic-based sensibilization improved the sensitivity to a single copy. This biosensor is simple and portable, with significant potential for rapid on-site screening.