In this work, a novel molecularly imprinted electrochemical sensor of dopamine (DA) has been fabricated with multi-walled carbon nanotubes spaced graphene aerogels (MWCNT/GAs) as the sensing substrate and polypyrrole (PPy) as the molecularly imprinted polymer (MIP). Morphological characterization showed that the MWCNTs were well dispersed on the graphene walls of the aerogels and the spaced GAs exhibited an outstanding loose structure and large effective surface area. Moreover, the introduction of conductive MWCNTs greatly increased the electrical conductivity and electrochemical performance of the composite aerogel. Benefiting from these features, the MWCNT/GAs showed significantly enhanced electrocatalytic activity for DA. Additionally, the MIPs as recognition elements were used for the selective detection of DA. The effects of various experimental parameters, including the volume ratio of the amount of functional monomer to that of template molecules, number of electropolymerization cycles, incubation time and pH of supporting electrolyte were tested and optimized. Under the best conditions, the MIP/MWCNT/GAs electrode could detect DA at concentrations down to 1.67 nM (S/N = 3) with a wide linear range from 5 nM to 20.0 μM. Moreover, the sensor exhibited specific selectivity and good stability. The developed sensor was successfully used for detecting DA in serum, suggesting that the as-prepared sensor could be used for determining the concentration of DA in complex real samples.