Body fluids contain a large number of disease markers including proteins, exosomes and cells, the concentration of which indicates the health status of a body system and can be hence applied to predict the degree of seriousness of a disease. However, the content of disease markers is relatively low. For solving this problem, a variety of pretreatment methods have been developed, among which aptamer-based nanomaterials hold great potential for biomarker capture because of various natural properties of nano-substrates such as high specific surface area, as well as the high affinity of aptamer towards target and the higher stability than antibody. In this review, we summarized the recent aptamer-based nanomaterials for the separation and analysis of different biomarkers including proteins, exosomes and cells. More specifically, the standard of classification description was based on the applied substrates including magnetic substrates and non-magnetic substrates. Moreover, the perspective of aptamer-based nanomaterials was discussed.