Herbicide-tolerant genetically modified soybean DBN9004, independently developed in China, was granted the agricultural genetically modified organism (GMO) safety certificate in 2021, demonstrating extensive application prospects. To provide prompt and reliable technical support for the GMO biosafety supervision of this variety, loop-mediated isothermal amplification (LAMP) technology was employed in this study. A set of LAMP amplification primers targeting the 3′-end boundary sequence of DBN9004 was designed to establish a rapid detection method for DBN9004 with an amplification time of approximately 45 min. This system effectively distinguished DBN9004 from other genetically modified soybean varieties, demonstrating strong specificity. Furthermore, detection sensitivity was 10 fg•μL-1 for recombinant plasmids containing DBN9004 sequences, 1 ng•μL-1 for DBN9004 genomic DNA, and 0.5% for positive mixed samples. The results demonstrate that this system offers several advantages, including a short processing time and high specificity and sensitivity, thereby playing a critical role in advancing onsite nucleic acid detection technology for genetically modified products of this soybean variety. Therefore, this system provides a practical and reliable technical foundation for the rapid screening and biosafety regulation of DBN9004.