Background: Extracellular vesicles, particularly CD63+/CD9+ Mesenchymal Stem Cell Exosome (MSC-Exo), have emerged as crucial mediators of intercellular communication and potential therapeutic agents, including regenerative medicine and immunomodulation. However, the precise isolation and purification of MSC exosomes pose critical challenges. Tangential Flow Filtration (TFF) has gained recognition as an efficient exosome isolation method, offering scalability and versatility. In this study, we address the pressing need for standardized exosome isolation methods by comparing two distinct TFF-based protocols for isolating CD63+/CD9+ MSC exosomes based on filter size pore order. Methods: MSC-Exo were conducted from the Stem Cell and Cancer Research Laboratory (SCCR Indonesia), which were then processed through TFF using different filter sizes and orders. There are two filtration methods compared, first, MSC-Exo was filtered with 1000-5-500-300-100-50-10-5 filter order. Second procedure, MSC-Exo was filtered using 1000-500-300-100-50-10-5 filter order. Result: Flow cytometry analysis revealed variations in the percentage of CD63+/CD9+ in the MSC-Exo based on filter order. The results indicate that the choice of filter order significantly influences the size range with the highest concentration of CD63+/CD9+ MSC-Exo. Conclusion: This research underscores the importance of optimizing TFF-based isolation methods for CD63+/CD9+ MSC exosomes, especially in the order of filter pore size.