A portable sensor platform for the detection of small molecular species is crucial for the on-site monitoring of environmental pollutants, food toxicants, and disease-related metabolites. However, it is still extremely difficult to find highly selective and sensitive sensor platforms for general small molecular detection. Herein, we report aptamer sandwich-based carbon nanotube sensor strategy for small molecular detection, where aptamers were utilized to capture target molecules as well as to enhance the sensor signals. We successfully demonstrated the detection of non-polar bisphenol A molecules with a 1 pM sensitivity. Significantly, our sensors were able to distinguish between similar small molecular species with single-carbon-atomic resolution. Furthermore, using the additional biotin modification on labeling aptamer, we enhanced the detection limit of our sensors down to 10 fM. This strategy allowed us to detect non-polar small molecular species using carbon nanotube transistors, thus overcoming the fundamental limitation of field effect transistor-based sensors. Considering the extensive applications of sandwich assay for the detection of rather large biomolecules, our results should open up completely new dimension in small molecular detection technology and should enable a broad range of applications such as environmental protection and food safety.