A combination of Terahertz (THz) emission and aptamer technologies has a crucial impact on the highly sensitive and rapid detection of small toxic molecules such as microcystin-LR (MC-LR). THz chemical microscope (TCM) is a unique THz aptasensor that has been successfully used for monitoring MC-LR molecules in buffer and complex samples. Our results show that our TCM aptasensor has an excellent detection limit of 50 ng/L as well as the assay time is about 15 min. Compared with other biosensors such as surface plasmon resonance (SPR), our TCM aptasensor provides a rapid and sensitive assay.