BackgroundChloramphenicol (CAP) is a broad-spectrum antibiotic, and its continuous use in human medicine, livestock has resulted disturbances in ecosystem stability. The complex background and low concentration of CAP in aquatic environments present significant scientific challenges for its sensitive detection. Currently detection techniques such as high-performance liquid chromatography (HPLC) and gas chromatography-mass spectrometry (GC-MS) are hindered by their complex procedures and high costs. Surface-enhanced Raman spectroscopy (SERS), due to its unique ability for fingerprint recognition, has emerged as a powerful tool for analysis and detection. However, it is often limited by the low kurtosis expression of the target. ResultThe water-soluble explosive polyethylenimide grafted calcium carbonate (PEI@CaCO3) microcapsule was utilized to encapsulate the signal probe Ag@4-NTP and combine it with a semiconductor SERS substrate Zn0.995Ce0.005O, enabling ultra-sensitive detection of CAP through a signal attenuation strategy. Moreover, magnetic molecularly imprinted polymers (MMIP) and nucleic acid aptamers were employed as capture probes for achieving rapid and direct magnetic separation, followed by layer-by-layer assembly to construct the sensor probe. In the presence of CAP, the aptamers and rMMIPs selectively recognized the target, forming a PEI@CaCO3@Ag@4-NTP@Apt@CAP@rMMIPs "sandwich" structure (Microcapsule@Apt@rMMIPs). After multiple magnetic separations, the "igniter" EDTA solution was added, causing the CaCO3 capsules to rapidly "explode" and release a significant amount of Ag@4-NTP. This was then applied to the "signal booster" semiconductor SERS substrate. Under optimal conditions, this method exhibited a detection range of 1.0 × 10−5 M to 1.0 × 10−15 M, with a detection limit of 6.84 × 10−16 M. SignificantThe unite of magnetic MIP and nucleic acid aptamer to form a “sandwich” structure, in combination with a semiconductor SERS substrate, not only enhances the sensor's sensitivity but also offers significant economic advantages. Moreover, this innovative technology holds great promise for accurate and highly sensitive detection of pollutants in complex environments.