The use of magnetic nanoparticles (MNPs) in sample preparation has gained much attention. Easyto-handle property of MNPs has provided a great promising solution for lab automation. Laboratory robotics and workstations based on magnetic separation are in rapid development process, and increasing efforts are debited for their practical applications in clinical methods. To increase the processing throughput and reduce the risk of cross contamination, we developed a multifunctional module to optimize the workflow of magnetic nucleic acid separation in automated workstation. Three functions (magnetic separation, heating, and shaking) were elaborately combined into this device, by which the 96-well plate-based sample preparation can be completed on site without transferring the plate to other auxiliary modules. Test experiments were carried out on this platform. It was shown that this multifunctional device could cooperate well with our pipetting system, and this new platform exhibited its ability to meet the demands for high-throughput sample preparation.