Using cyanine dyes supramolecular as molecular probes to mark FA has important significance in life sciences and pharmaceutical chemistry, which can detect FA as drug efficacy mechanism and the change in physiological activity. In the present paper, we investigated supramolecular assembly and chiral inducement of cyanine dyes template by FA with absorption and circular dichroism (CD) spectra. The result suggests that FA can induce cyanine dyes from J-aggregation to monomer along with different colors change and has strong affinity with cyanine dye monomer.The template of FA not only can translate the chirality of MTC H-aggregation to other two states, but also induce ETC J-aggregation to molecular rearrangement and form left-handed helix of J-aggregates.Besides, the association of PTC with FA, i.e. binding to FA gave rise to the J-aggregation CD signals.Meanwhile, it was inferred that the meso substituent of cyanine dyes play an important role in the interaction between FA and the J-aggregation: the smaller the meso substituent, the higher the affinity interacted with FA.Clearly, the binding abilities between cyanine dyes and FA follow the order of MTC>ETC>PTC.These results support that the cyanine dyes supramolecular aggregates can be used as a kind of excellent molecular probes for specific recognition of FA and achieve the effect of visual inspection.