An electrochemical sensor was explored for recognizing 3,4-dihydroxyphenylalanine (DOPA) enantiomers based on L-cysteine covalently binding with the multi-walled carbon nanotubes functionalized with 3,4,9,10-perylene tetracarboxylic acid (MWCNTs-PTCA-Cys). Here two different ways of square wave voltammetry (SWV) and cyclic voltammetry (CV) were utilized to investigate the stereospecific interaction between the MWCNTs-PTCA-Cys nanocomposite and DOPA enantiomers. The D-DOPA and L-DOPA exhibited different response in both CV and SWV, in addition, the difference in SWV was more obvious and reached to 264.9 μA, suggesting that the enantiomers could be successfully distinguished by MWCNTs-PTCA-Cys nanocomposite, and the selection of electrochemical technique played an important role in enantioselective recognition. Under the optimum conditions, the detection limits of D-DOPA and L-DOPA were 2.5 μM and 4.6 μM (S/N = 3), respectively, with a linear range of 1.0 × 10−5 M to 5.0 × 10−3 M. This work provided a simple method to recognize and determine DOPA enantiomers with rapid response, excellent recognition ability, high sensitivity and good stability.