The detection and elimination of antibiotic contaminants, such as oxytetracycline (OTC), a broad-spectrum tetracycline antibiotic, would be of help in efficient environmental monitoring, agriculture and food safety tests. Nevertheless, currently available methodologies, which mostly rely on the chromatographic separation of OTC, suffer from low sensitivity and complicated processes. Thus, we report here on the design and synthesis of a fluorescent sensor based on molecularly imprinted magnetic halloysite nanotubes (referred to as MHNTs@FMIPs) for the effective detection and purification of OTC in actual environmental samples. The fluorescence of the MHNTs@FMIPs was quenched obviously upon loading with OTC, covering a linear concentration range of 10–300 nM with a limit of detection (LOD) as low as 8.1 nM. The imprinting factor is 4.47, indicating an excellent specificity. Furthermore, the MHNTs@FMIPs can be applied to the quantitative detection of OTC (5 cycles of 300 nM) in aquaculture wastewater and Yangtze River water, demonstrating their immense application potential.