In filamentous fungal fermentation, selecting suitable impellers and controlling fungal morphology are crucial for product yield. We previously demonstrated that the AGΔ-GAGΔ strain of Aspergillus oryzae, lacking both α-1,3-glucan (AG) and galactosaminogalactan (GAG), had improved hyphal dispersion, reduced culture viscosity, and increased recombinant protein production. Here, we applied computational fluid dynamics (CFD) using viscosity data to explore the importance of impeller design and strain engineering. High-performance impellers (HS100/HR100) were compared with the conventional flat-blade turbine and paddle (6FT/4FP). CFD analysis showed large gas cavities behind the blades and severe compartmentalization for both the wild-type and AGΔ-GAGΔ strains. HS100/HR100 had more homogeneous velocity and shear stress values than did 6FT/4FP. The AGΔ-GAGΔ strain had a wider shear stress distribution and reduced gas cavity in comparison with the wild-type strain. The simulation results agreed with measured volumetric oxygen mass transfer coefficients ( K_La) and mixing times. Transcriptional analysis during HS100/HR100 cultivation revealed upregulation of the TCA cycle genes in AGΔ-GAGΔ in comparison with the wild type. Our findings suggest that the combination of an optimized stirring system and the AGΔ-GAGΔ strain can significantly enhance mixing. Furthermore, the improved mixing properties of AGΔ-GAGΔ may contribute to higher recombinant protein yields through an increased population of metabolically active cells.