Mycotoxins are toxic secondary metabolites generated during the infection of agricultural products by fungus. The contamination of mycotoxins presents a major risk to the health of human and livestock. Thus, rapid and sensitive detection of mycotoxins in agricultural products is an urgent task. In this work, a new method for mycotoxins detection was established by combining molecularly imprinted polymer (MIP) with surface-enhanced Raman spectroscopy (SERS). Direct detection of aflatoxin B1 (AFB1) in corn and peanuts was accomplished according to the characteristic signals of the target molecules. In brief, Au nanoparticles (AuNPs) were encapsulated with an MIP layer for specific capture of AFB1. After optimization, the AuNPs@MIP hybrid nanomaterials enabled effective and selective adsorption of AFB1, following with qualitative and quantitative SERS detection according to the characteristic bands in the obtained spectra. The limit of detection for AFB1 was as low as 0.1 ng/mL, which was significantly lower than the maximum residue levels set by the Chinese government. Spiking experiments were carried out to examine the performance by employing corn and peanuts as the real sample, and the recovery rates were in the range of 89.6~107.3%. Thus, this method can be used for rapid and sensitive screening of AFB1 contamination in grains and nuts. The proposed study demonstrated the major advantages of combining MIP and SERS for the detection of food contaminants, including high sensitivity, selective recognition and enrichment of the target, rapid assay, ease of operation, and low cost. Therefore, it should be considered as a promising platform for rapid screening and early warning of various contaminants in agricultural products.