The automatic and rapid nucleic acid extractor (NAE) has been developed at our laboratory with the help of multi-axis motion control technology, magnetic separation technology and multiplexing temperature control technology. This report introduces the designing protocol and the application in nucleic acid purification of NAE. The range of temperature control is from room temperature to 99 C, and the precision is about ±0 5 C. Moreover, the system is easy and friendly to operate and the extraction process of most samples can be finished within 30 min. The volume of sample should be 30-1000 L and 16 samples can be treated simultaneously. The motion control, mechanical structure, and experimental formulation also were optimized to increase the yield and purify the products. In the end, the yield and purification of 16 experimental groups from one hepatic cellular cancer (HCC) sample suggest that the developed system is stable and reliable. And high yield and purification of nucleic acid from three kinds of samples were obtained successfully with the system.