In this work, an electrochemical sensor was designed for trace monitoring of bisphenol A (BPA) by decorating a hybrid bilayer molecularly imprinted membrane (MIM) on a multi-walled carbon nanotube-modified glassy carbon electrode. When BPA in the MIM was eluted, a composite molecularly imprinted electrochemical sensor was constructed. Under optimal conditions, the developed sensor showed two linear relationships between Δ I p and BPA concentration in the range of 0.04 μM to 8 μM, as well as good selectivity and stability, and was also applied to detect BPA in water samples with desirable recoveries ranging from 92.0% to 107.0%.