Vibrio parahaemolyticus is a common food borne pathogen. In order to solve the problems of complex steps and long detection period of Vibrio parahaemolyticus, a magnetic bead extraction and PCR combined technique was developed for rapid detection of Vibrio parahaemolyticus in food. Firstly, Fe3O4 magnetic beads were prepared by alkaline coprecipitation method, and then Fe3O4@SiO2 magnetic beads were prepared by hydrolysis of tetraethy orthosilicate at room temperature. The effects of tetraethyl orthosilicate addition on the particle size and magnetic properties of Fe3O4@SiO2 magnetic beads were discussed. The effects of particle size of Fe3O4@SiO2 magnetic beads and pH value of extraction system on the binding ability of Fe3O4@SiO2 magnetic beads to DNA were analyzed. The results showed that the optimal particle size of Fe3O4@SiO2 magnetic beads combined with Vibrio parahaemolyticus DNA was 105.89nm, and the SiO2 layer of Fe3O4@SiO2 magnetic beads was 25nm. Under these conditions, Fe3O4@SiO2 magnetic beads had smooth surface, good dispersion and high saturation magnetization. The separation of Vibrio parahaemolyticus DNA and impurities could be completed in 10 seconds under the action of magnetic field. The extraction rate of Vibrio parahaemolyticus DNA was as high as 80% (pH value of extraction system was 5.0). The optimized Fe3O4@SiO2 magnetic beads were used for DNA extraction. Combined with PCR, 92 commercial aquatic samples (32 prawns, 25 oysters and 35 mussels) were screened for Vibrio parahaemolyticus. The results showed that the DNA extracted by Fe3O4@SiO2 magnetic beads could be directly used for PCR detection, and 17 samples were positive for Vibrio parahaemolyticus. Compared with the national standard detection method (GB 4789.7—2013), the detection time was shortened from one week to 4 hours, which improved the detection efficiency of Vibrio parahaemolyticus. Magnetic bead extraction combined with PCR could detect a variety of microbial strains in different foods. This study might provide a new practical method for rapid detection of microorganisms in food.