The geometric configuration of fiber bundles plays a critical role in gas transfer for membrane oxygenators; however, experimentally studying its impact on gas transfer distribution is challenging. This study numerically examines oxygen and carbon dioxide transfer processes in a mini-oxygenator with a fiber bundle, focusing on the effects of inlet blood flow rate, fiber bundle cross-sectional area, fiber spacing, and wall effects. The numerical model, validated against existing data, was used to analyze blood gas parameter distribution under varying conditions. The findings indicate that an increase in blood inlet flow rate delays oxygen saturation and reduces the partial pressure of oxygen at the same location within the fiber bundle. Furthermore, the cross-sectional area perpendicular to the inlet flow direction, when maintaining a consistent fiber bundle volume, noticeably impacts gas exchange performance. Fiber spacing strongly affects carbon dioxide–related parameters but has negligible impact on oxygen-related parameters. The wall effect on gas transfer is limited to the outermost fiber layer adjacent to the wall. These studies elucidate the relationship between gas transfer performance and geometric factors, thereby providing insights for optimizing fiber bundle geometry in the design of membrane oxygenators to enhance efficiency and effectiveness.