Herein, we report a novel route to prepare polymorphic carbon dot fluorescent probes via the evaporation-induced self-assembly of glutaraldehyde and carbon dots, which first usually form carbon nanoclusters which then could self-assemble to form carbon nanocrystals, nanospheres or nanofibers in different ionic strength solutions at room temperature. The aldehyde functionalized polymorphic C-dot fluorescent probe can easily covalently bond with amino groups on proteins.