A simple and reliable chiral sensing platform for enantioselective recognition of lysine (Lys) enantiomers based on a nanostructured composite (NC) via the electrochemical impedance spectroscopy (EIS) technique was described. The NC has been successfully synthesized through covalent linkage among the semiconductor 3,4,9,10-perylenetetracarboxylic acid (PTCA), thionine (Thi) and chiral selector L-N-tert-butoxycarbonyl-O-benzylserine (L-BBSer). The stepwise synthesis process of the NC was characterized by scanning electron microscopy (SEM), X-ray photoelectron spectroscopy (XPS) and EIS. The enantioselective interaction assay between NC modified glassy carbon electrode and lysine enantiomers relied on EIS technology. As a prototype example, good recognition results were obtained from the difference of electron transfer resistance (ΔR_et), where ΔR_etD was larger than ΔR_etL and linear responses in ΔR_et were found for Lys enantiomers ranging from 100 nM to 10 mM with a detection limit of 33 nM (S/N = 3). In addition, the results of analyzing another four amino acids revealed the specificity of the proposed sensor. The developed sensor with the advantages of simple preparation, long-term stability, good sensitivity and commendable selectivity, holds great potential application for the nanostructured composite adulterated with a chiral selector in chiral bio-electroanalysis.