In fermentation of filamentous fungi, selecting suitable impellers and controlling fungal morphology are crucial for product yield. Previously, we revealed the AGΔ-GAGΔ strain of Aspergillus oryzae, lacking both α-1,3-glucan (AG) and galactosaminogalactan (GAG), showed improved hyphal dispersion, reduced culture viscosity, and increased recombinant protein production. Here, we used computational fluid dynamics (CFD) to explore the importance of impeller selection. High-performance impellers (HS100/HR100) were compared with the conventional flat-blade turbine and flat-blade paddle combination (6FT/4FP). CFD analysis using viscosity data of the wild-type strain showed gas cavities formed behind the 6FT/4FP blades, with flow velocities and shear stresses concentrated around the impellers; in contrast, HS100/HR100 displayed a broader and more evenly spread range of flow velocities and shear stress values. CFD analysis comparing the mixing properties of AGΔ-GAGΔ and wild-type strain cultures agitated by HS100/HR100 demonstrated that slipping occurred at the impeller periphery–wall boundary in the wild-type culture, while AGΔ-GAGΔ exhibited a wide shear stress distribution and reduced gas cavity formation. The simulation results agreed well with measured volumetric oxygen mass transfer coefficient ( K_La) and mixing time. These findings suggest that an appropriate stirring system, combined with the AGΔ-GAGΔ strain, can drastically improve the mixing characteristics in filamentous fungal fermentation.