Macrocycle‐induced formation of pure organic supramolecular aggregates is a challenge that has attracted considerable attention from researchers in the fields of chemistry, biology, and materials science. In particular, aggregation induced by water‐soluble cyclodextrins and calixarenes, which are two classic of macrocycles with a hydrophobic cavity and a hydrophilic external surface, has attracted interest because these host molecules can form aggregates with guest molecules via various noncovalent interactions, including hydrophobic interactions, van der Waals forces, hydrogen bonds, and electrostatic interactions. In this review, we focus mainly on some impressive recent progress, both by our group and other groups, on the construction of cyclodextrin‐ and calixarene‐based organic supramolecular aggregates, control of their topological morphology, and their use for biological applications such as molecular recognition and bioimaging, photodynamic therapy, light‐harvesting energy transfer, and targeted drug delivery. We also discuss shortcomings of the current reported results and future prospects for the development of multifunctional organic supramolecular aggregates for use in various fields.