Transmission electron microscopy (TEM) is a unique and powerful tool for observation of nanoparticles. However, due to the uneven spatial distribution of particles conventionally dried on copper grids, TEM is rarely employed to evaluate the spatial distribution of nanoparticles in aqueous solutions. Here, we present a microchip nanopipet with a narrow chamber width for sorting nanoparticles from blood and preventing the aggregation of the particles during the drying process, enabling quantitative analysis of their aggregation/agglomeration states and the particle concentration in aqueous solutions. This microchip is adaptable to all commercial TEM holders. Such a nanopipet proves to be a simple and convenient sampling device for TEM image-based quantitative characterization.