With the higher and higher application level of medical technology, more and more genetic diseases have been diagnosed. Nucleic acid, as an important genetic material, has been found to have important functions in the storage and transmission of the genetic information in the replication and synthesis of proteins. As the first step in nucleic acid detection experiments, nucleic acid extraction performance is associated with the purity of target nucleic acid samples, which is very important for the downstream steps. In this paper, we employed the magnetic bead for extracting nucleic acids based on the platform of large liquid handling workstation and designed a matching magnetic separation module. It was shown that the temperature control block designed in this paper has reliable stability, high accuracy by using the incremental PID algorithm, with the control accuracy up to ±0.5 °C, and the control stabilization time is about 90 s, which can satisfy the experimental requirements. Besides, the average magnetic bead transfer rate of this module was further verified by mimicking the manual magnetic bead nucleic acid extraction process. The results proved that the module has an excellent performance with the average magnetic bead transfer rate greater than 95% and the magnetic bead transfer rate in each well greater than 90%, which could be consistent with the experimental indictors of nucleic acid extraction.