This disclosure relates to a multi-stage method and apparatus for purifying extracellular vesicles using an aqueous two-phase system, in which extracellular vesicles mixed and contaminated with proteins can be isolated and purified in a large amount at high purity within a short time through a multi-stage purification process using an aqueous two-phase system, thereby removing 95% or more of proteins and obtaining high-purity extracellular vesicles, resulting in very high processing efficiency compared to conventional techniques. In particular, the method of the disclosure does not require an expensive device or material such as an ultracentrifuge or an antibody, and can be performed at low cost and is thus economical and highly competitive. Furthermore, the extracellular vesicles thus isolated and purified can be employed in analysis methods such as RT-PCR or western blot, and can be utilized for research fields and disease diagnosis using the same.