In view of the great threat of chloramphenicol (CAP) to human health and the fact that a few producers have illegally used CAP in the food production process to seek economic benefits in disregard of laws and regulations and consumer health, we urgently need a detection method with convenient operation, rapid response, and high sensitivity capabilities to detect CAP in food to ensure people’s health. Herein, a molecularly imprinted polymer (MIP) electrochemical sensor based on a dual-signal strategy was designed for the highly sensitive analysis of CAP in milk. The NiFe Prussian blue analog (NiFe-PBA) and SnS2 nanoflowers were modified successively on the electrode surface to obtain dual signals from [Fe(CN)6]3−/4− at 0.2V and NiFe-PBA at 0.5 V. SiO2-COOH@MIPs that could specifically recognize CAP were synthesized via thermal polymerization using carboxylated silica microspheres (SiO2-COOH) as carriers. When the CAP was adsorbed by SiO2-COOH@MIPs, the above two oxidation peak currents decreased at the same time, allowing the double-signal analysis. The SiO2-COOH@MIPs/SnS2/NiFe-PBA/GCE sensor used for determining CAP was successfully prepared. The sensor utilized the interactions of various nanomaterials to achieve high-sensitivity dual-signal detection, which had certain innovative significance. At the same time, the MIPs were synthesized using a surface molecular imprinting technology, which could omit the time of polymerization and elution and met the requirements for rapid detection. After optimizing the experimental conditions, the detection range of the sensor was 10−8 g/L–10−2 g/L and the limit of detection reached 3.3 × 10−9 g/L (S/N = 3). The sensor had satisfactory specificity, reproducibility, and stability, and was successfully applied to the detection of real milk samples.