A novel dual-modal sensing interface was constructed for the electrochemical/colorimetric dual-modal sensing of aloe-emodin (AE). Fe3O4 micro-particles were directly synthesized on a multi-layer exfoliated graphite paper (EGP) by the in-situ hydrothermal approach, which was subsequently modified with a layer of molecularly imprinted polymer (MIP) using pyrrole and aloe emodin (AE) as monomer and template, respectively. Due to the specific recognition ability of MIP, the prepared sensing interface showed a good selectivity to AE. The advantages of the multi-layer EGP, such as the large surface area and the excellent conductivity, enabled the sensing interface to sensitively detect AE based on the electrochemical mode. Moreover, due to the peroxidase-like activity of the modified Fe3O4 micro-particles, 3,3′, 5,5′-tetramethyl-benzidine can be oxidized to deep blue by the prepared sensor in the presence of H2O2. However, the rebound AE molecules in imprinted cavities blocked the activity of Fe3O4 micro-particles and caused the light blue of color, which achieved the visual colorimetric assay of AE with the good sensitivity and selectivity. With the merits of easy preparation, good selectivity, and high sensitivity, the present electrochemical/colorimetric dual-modal strategy would greatly broaden the practical application of the molecular imprinting.