In this paper, magnetic molecularly imprinted polymers-surface-enhanced Raman spectroscopy (MMIPs-SERS) for rapidly analyzing acetamiprid and thiacloprid in agricultural products has been firstly developed. The magnetic imprinted polymers were obtained by polymerizing the imprinted layers on the surface of magnetic nanoparticles. The polymers were detailed characterized by using series of analytical techniques, and their adsorption and recognition performance were validated by adsorption tests. The results showed that the magnetic molecularly imprinted polymers possessed typically core-shell structure and exhibited class-specific recognition, fast adsorption saturation (only 1 min), and good magnetic separation performance towards targets. The adsorption and desorption conditions for MMIPs-SERS detection system were carefully investigated. Under optimum conditions, the good linear detection range of 1∼20 μg/g with LODs of 23.7–68.8 ng/g for acetamiprid and thiacloprid in peach and pear samples was obtained. Through the reusable and spiked experiments, the developed MMIPs-SERS method based on Au NPs as enhanced substrate was validated to be highly sensitive, accurate, efficient and applicable in analyzing neonicotinoids from pear and peach samples. This study provided a rapid and simple detection method for neonicotinoids with effective separation and detection properties based on the synergistic effect of imprinted polymers and SERS. More importantly, this developed method have good application potential in rapid analyzing field for neonicotinoids due to the amazing rapid adsorption time for extracting targets from complex food matrix (only 1 min).