Exosomes are a unique pathway of cell-cell and cell-matrix communication media, which has aroused increasing research interest. In cell culture systems, to maintain normal physiological function of the cell, fetal bovine serum (FBS) is a nearly indispensable additive in the cell culture medium. The consequent problem is that the serum contains a large number of exosomes, several times more than the specific exosomes in the study that need to be targeted, which causes interference in the quantitation and analysis of specific exosomes. Therefore, many studies applied differential centrifugation or density gradient centrifugation to remove the serum exosomes from the culture medium. In this study, we analyzed the decrease percentage of the exosomes from medium with the addition of different amount of FBS by fluorescence activated flow cytometry (FACS). We found that when cell culture medium was supplemented with 2% FBS, the amount of exosome dropped 30.6% after differential centrifugation. When supplemented with 5% FBS, the amount of exosome dropped 32.4%. Differential centrifugation brought no significant difference between the decreasing of the amount of the exosomes in media with different percentages of the FBS, suggesting that the maximum amount of the exosomes can be removed by differential centrifugation is around 30%, while there is still 70% interference remains. Therefore, human umbilical vein endothelial cells (HUVECs) culture system was used to test the minimum FBS to maintain normal cell function and exosome secretion. A serum substitute XerumFree without any biological components was used to replace partial of the FBS. Our results showed that the ratio of 15 (XerumFree) to 1 (FBS) is the best condition to maintain normal cell function and exosome secretion while the interference of FBS was the minimum (less than 2%). The results from the study provide useful reference and a solid basis to exosome related research.