In this paper, a superparamagnetic Fe3O4 core encapsulated into a metal-organic framework shell, Fe3O4@MIL-100(Fe), was successfully synthesized taking advantage of layer-to-layer method. The thickness of the shell can be controlled by self-assembly cycles between FeCl3·6H2O and 1,3,5–benzenetricarboxylic acid (H3BTC). The composites were characterized by Powder X-ray diffracrion (XRD), transmission electron microscopy (TEM), fourier transform infrared spectroscopy (FTIR) and N2 adsorption/desorption isotherms. Then, the synthesized material was firstly used to fabricate a novel electrochemical sensor for chlorogenic acid (CGA). Under the optimal conditions, this electrochemical sensor can detect CGA quantitatively in the range of 0.1–10.0 μmol L−1 and 10.0–460 μmol L−1. The limit of detection (LOD) can be as low as 0.05 μmol L−1. Considering there are little common interfering materials, this novel chlorogenic acid sensor was further applied in real samples to detect the content of CGA.