A localizing and tracking system based on magnetic sensor array is proposed to realize the real time localizing and tracking of the micro diagnosis and treatment devices in human Gastrointestinal tract (GI tract). This localizing system uses magnetic dipole model as mathematic model for magnetic field of permanent magnet and uses a 4×4 three axis magnetic sensor array to measure the magnetic field. A control circuit and an USB adaptor are used to transport the signal to the computer,then, the position and posture parameters of the magnetic object are computed by a nonlinear optimization method. Finally,a program is developed to display and save the localization result in real time. The real experimental results show that the average localization error is less than 7 mm, the average orientation error is less than 6°when the capsule is 150 mm away the sensor array plane. At the same time, this localizing system is able to track the capsule that moves among a simulated intestinal tract.Moreover, the localization error is not sensitive to glass, plastic, clothes, water and human body. It is conclusion that this localizing system is able to realize the real time localizing and tracking of the micro diagnosis and treatment devices in human GI tract.