Tetracycline is extensively used as an antibiotic in animal husbandry, and there arose an increase in antibiotic resistance genes in the environment, posing a threat to human health. Motivated by this, a magnetic molecularly imprinted material based on synergistic recognition (1 + 1>2) was constructed and coupled with high-performance liquid chromatography to detect ultra-trace tetracycline in complicated samples. In this case, the molecularly imprinted polymers were synthesized via a “one-pot” method and acted as recognition elements on the surface of silica-coated ferroferric oxide particles. Aptamers and β-cyclodextrin, as functional monomers, had a synergistic effect on the recognition of tetracycline and the synergistic recognition factor was 1.7. Meanwhile, the material exhibited high selectivity to tetracycline with an imprinting factor of 7.6. In addition, compared to being modified on the surface, the stability of the aptamers was effectively improved by cross-linking in the molecularly imprinted polymer framework. Relevant experimental conditions, such as buffers, concentration of magnesium ions and adsorption time, were optimized. As a result, the method showed a limit of detection of 1.0 μg L−1 and the linearity range of 0.005–0.5 mg L−1, as well as certain reproducibility and stability. Furthermore, when applied for the analysis of animal feed samples, a significant reduction of matrix interference was observed with satisfactory recoveries (85.0–111.5%), which emphasized the good accuracy and practicability of the established method. For these advantages, the proposed method represents a versatile and powerful tool for the separation and detection of small molecule compounds in complicated real samples.