Based on density differences of different subpopulations of exosomes, two kinds of micro-vesicles with different densities were captured from urine by a modified sucrose density gradient ultracentrifuge separation method. Verified by transmission electron microscope (TEM) and western blot, the results showed these two kinds of micro-vesicles were all exosomes. And these two kinds of exosomes were analyzed by TEM, 2D electrophoresis (2DE), and capillary zone electrophoresis (CZE), respectively. The results of TEM showed these two exosomes with different densities have different morphological characteristics, and some tiny proteomic differences were shown in the results of 2DE of these two exosomes. At the same time, the CZE results displayed these two kinds of exosomes possessed different retention times, indicated that they may have different electrification property and particle weight. These results may attribute to their different origins. This work may provide a preliminary experience for the origin-tracking study for urinary exosomes, and would be more useful for future targeted biomarker discovery.