Abstract Within the legal framework of a quantitative labeling system for GM events in multiple countries, it is essential to accurately identify and quantitatively analyze specific GM transformation event. This study has established qualitative and quantitative multiplex detection methods for four authorized GM soybean events, enabling precise identification of target GM ingredients in mixed samples with as little as 0.1% (w/w). Additionally, the optimal systems could be compatible with the 3-plex digital PCR platform for quantification. The limit of detection (LOD) and limit of quantification (LOQ) are 20 copies and 10 copies, respectively. Furthermore, the 3-plex digital PCR methods are compatible with droplet-based digital PCR platforms and original real-time PCR. They allow for higher throughput and increased sensitivity in the identification and quantification of GM soybean events. These findings provide robust technical support for regulatory oversight within the biotechnology industry.