Human umbilical cord-derived mesenchymal stem cells (hUC-MSCs) are widely utilized in the field of regenerative medicine, particularly in cell therapy and tissue engineering. However, their application and development are hindered by limitations in cell expansion efficiency. When hUC-MSCs are cultured in suspension while attached to microcarriers, they tend to aggregate, and adjusting operational parameters fails to resolve the conflict between shear and aggregation. The microenvironment created by the original impeller is not suitable for cell growth. In this study, computational fluid dynamics (CFD) simulations were employed to investigate the flow field structure generated by the original impeller in the commercial spinner flasks. It was found that the flow field structure were unsuitable for the expansion of cells prone to aggregate. Consequently, a new impeller was designed to alter the flow field structure, aimed to promote aggregate suspension while maintaining a similar shear rate at the same rotation speed. Compared to the original impeller, the newly designed impeller demonstrated significant improvements. Notably, it reduced the size of aggregates, increased maximum cell density, and preserved cell stemness during cell expansion. Combining simulation results with experimental data, this study reveals that the degree of suspension of aggregates played a critical role in determining aggregate size. Additionally, the level of cell stemness was determined by modulating shear rate and the degree of aggregate suspension.