This article primarily develops a new technology for the rapid large-scale screening of isoliquiritigenin-transforming strains based on the MTHM (microplate reader-TLC-HPLC-UPLC-MS) method. ISO is a chalcone compound with potential pharmacological activity, and its rich substitution sites on the benzene ring provide a solid foundation for structural modification and drug development. This study screened approximately 1500 strains and employed a microplate reader, thin-layer chromatography, high-performance liquid chromatography, and mass spectrometry to verify the transformation products, identifying 15 strains with significant transformation capabilities. This study demonstrates that the optimized MTHM method is efficient and reliable, capable of rapidly detecting subtle structural changes in flavonoids before and after microbial transformation. During the transformation process, bioactive flavonoid compounds, such as amentoflavone and 5'-methoxyflavonoid, were discovered. Additionally, the experiments revealed that Czapek medium, modified Martin medium, and LB medium exhibited high efficiency in screening transforming strains. This research provides new technical approaches for ISO structural optimization and drug development while highlighting the important application potential of microbial transformation in natural product development. Future studies could further explore the metabolic potential of these strains, optimize transformation conditions, and promote the application of ISO in the medical field.