Air traps play a critical role in controlling air bubbles and clots in hemodialysis systems. The quality of the micro‐filter, an injection molded part inside the air trap, influence the potential risk of passing emboli to the patient, which can result in serious complications. The aim of this work is optimizing the simulated injection molding process of a dialysis micro‐filter based on minimizing the shrinkage, part weight, and clamping force to maximize the part quality. First, micro‐computed tomography is used to diagnose defects of a typical micro‐filter due to the molding process. Next, the injection molding of micro‐filter is simulated via Autodesk Moldflow Adviser (AMA) to obtain the responses, and the interactions of the process factors are then determined by central composite design (CCD). The injection time is the most significant influence on the responses. Multi‐response optimization results for the equal weights of the responses show the minimum shrinkage, part weight, clamp force of 8.84%, 0.744 g and 0.625 tonne, respectively, with composite desirability of 0.61. Finally, the predicted values using regression models are successfully validated via AMA, offering the optimal process settings to produce high quality dialysis micro‐filter to reduce the risk of passing emboli to patients.