To address the challenges such as complex operation, long detection time and expensive equipment in nucleic acid amplification-based techniques for the detection of genetically modified (GM) grains, this study developed an efficient and rapid method that requires no purification or dilution for nucleic acid extraction from maize and soybean. It selected efficient and specific GM universal element primers and established a rapid loop-mediated isothermal amplification (LAMP) system and an anti-contamination system for GM maize and soybean. Furthermore, a rapid and visual detection method was developed based on the clustered regularly interspaced short palindromic repeats/CRISPR-associated proteins (CRISPR/Cas) system. The proposed method could be complected within 45 min, with a detection limit of 0.1% for representative transgenic components in GM soybeans and maize. This method enables rapid and precise detection of GM grains, thereby helping to enhance regulatory capacity for grains and holding great promise for future applications.