Extracellular vesicles (EVs) are lipid bilayer-delimited particles secreted by cells and are regarded as a promising class of nanocarriers for biomedical applications such as disease diagnosis, drug delivery, and immunomodulation, as they carry biomarkers from the parental cells and can also transport diverse cargo molecules between cells. Surface functionalization of EVs can help obtain detectable signals for their quantification and also add various properties for EV-based delivery. Aptamers are specific oligonucleotides selected as artificial antibodies that could serve as 'cruise missiles' to target EVs for diagnosis or as navigators to bring EVs to lesions for treatment. DNA logic devices or nanostructures based on aptamers are intelligent designs to endow EVs with additional features, such as multi-target disease diagnosis in one pot and promoting retention of EVs in complex disease microenvironments. Oligonucleotides or DNA nanostructures composed of natural nucleic acids can be easily degraded by nuclease in the biological sample which limits their applications. Thus, the oligonucleotides composed of artificial nucleic acids which are synthesized against degradation would be a potential strategy to improve their stability in vitro or in vivo. Herein, we review the methods for surface functionalization of EVs by nucleic acids and highlight their applications in quantification and targeted delivery towards disease diagnosis and therapy.