Objective：A localization system for multiple magnetic targets based on magnetic sensor rotation detection was studied，which was aimed at realizing human multiple capsule endoscopy positioning and nano-magnetic drug testing. Methods：A three-axis tunneling magnetoresistive sensor was used to make a circular motion near the magnetic source. Three sets of magnetic signals were acquired and transferred by three-dimensional coordinates. The position of the permanent magnet was solved using a positioning algorithm. Results：Through the preparation of LabVIEW PC program，the trajectory of two magnetic target tracking and motion curve storage and playback were achieved. Conclusion：The detection system has the advantages of good real-time，high precision and low cost，it has the potential application value for the positioning of multiple capsules in the human body and the detection of nano-magnetic drugs.