Driven by the urgent need for recognition and quantification of trace amino acids enantiomers in various biologic samples, we demonstrate for the first time an ultrasensitive electrochemical chiral biosensor for cysteine (Cys) based on magnetic nanoparticles (Fe3O4@PDA/Cu xO) as electrode units. d-Cys-Cu2+-d-Cys formed in the presence of cysteine exhibits strong stability and a shielding effect on the redox current of indicator Cu2+, which can be used to quantify and recognize d-Cys by square wave voltammetry. Simultaneous detection of d-Cys and homocysteine (Hcy) is achieved in the presence of other amino acids, demonstrating an excellent selectivity of the sensor. Moreover, aided by the enrichment treatment effect of magnetic micronanoelectrodes, an ultrahigh sensitivity up to 102 μA μM-1 cm-2 was achieved, the detection limit is reduced to picomolar level (83 pM) for d-Cys and can be used for the recognition of cysteine enantiomers. The proposed method has been verified by real sample analysis with satisfactory results. The results highlight the feasibility of our proposed strategy for magnetic micronanoelectrode sensor, electrochemical recognition, and quantification of d-Cys, which can be more broadly applicable than that with traditional electrode structures and further advance the field of electrochemical sensors.