Monodisperse carbon nanodots (MCNDs) having an identical composition, structure, shape and size possess identical chemical and physical properties, making them highly promising for various technical and medical applications. Herein, we report a facile and effective route to obtain monodisperse carbon nanodots 3.5 ± 0.9 nm in size by thermal decomposition of organosilane within the pores of monodisperse mesoporous silica particles with subsequent removal of the silica template. Structural studies demonstrated that the MCNDs we synthesized consist of ∼7-10 defective graphene layers that are misoriented with respect to each other and contain various oxygen-containing functional groups. It was demonstrated that, owing to their identical size and chemical composition, the MCNDs are formed via coagulation primary aggregates ∼10-30 nm in size, which are, in turn, combined into secondary porous spherical aggregates ∼100-200 nm in diameter. The processes of coagulation of MCNDs and peptization of their hierarchical aggregates are fully reversible and can be controlled by varying the MCND concentration or the pH value of the hydrosols. Submicrometer spherical aggregates of MCNDs are not disintegrated as the hydrosol is dried. The thus obtained porous spherical aggregates of MCNDs are promising for drug delivery as a self-disassembling container for medicinal preparations.