Most biologists think that AFM has only a limited use in biological research due to its inability to study other than surface structures. Therefore, a BIO-AFM system has been developed to combine both AFM imaging and fluorescence detection, which acts as a powerful tool for a better understanding of dynamic cell processes. In this study, based on a custom-made BIO-AFM system, the elasticity and ultrastructure of living periodontal ligament cells (PDLCs) were investigated. The cantilever probe with a micron-sized bead was used to exert nano-loading force onto the PDLCs. The related signal of NO was then recorded simultaneously. The results show that PDLCs hold strong networks of stress fibers as well as high elastic modulus value, exhibiting the ability for better counteracting the external forces. In the mechano-transduction studies, an initial increase and subsequent drop in intracellular NO response was found. Furthermore, NO may diffuse from a stimulated cell to adjacent cells. In conclusion, our single-cell nano-mechanical study provides a significant advancement in elucidating the magnitude, location, time scale, and biomolecular mechanisms underlying cell mechano-transduction.