Abstract:[Background] Filamentous fungi are a key group of host fungi in industrial fermentation. How to carry out high-throughput cultivation and screen out the efficient strains is an important direction of the research on industrial filamentous fungi. [Objective] To establish a high-throughput cultivation technology of filamentous fungi and evaluate its efficiency. [Methods] After studying the seed production, inoculation, cultivation, and detection of filamentous fungi, we established a microplate-based high-throughput cultivation technology and evaluated its performance with Myceliophthora thermophila. [Results] Compared with the traditional methods using either plate or shake flask for seed production, the microplate-based method increased the seed production by 24 folds, the spore production per unit area by 350%, and the transfer efficiency of liquid culture by 10-40 folds. Furthermore, a 96-well microplate-based high-throughput technique was developed for ethanol content determination. [Conclusion] The developed high-throughput technology increased the cultivation and detection efficiency of filamentous fungi by 1−2 orders of magnitude. This study lays a foundation for rapid screening of the target strains from a large number of variants with different traits and provides a reference for the research on filamentous fungi.