Magnetically manipulated untethered robot, such as an active wireless capsule endoscope, has shown great potential for controlled inspection inside the gastrointestinal tract. To enable the effective manipulation of the robot, real-time pose (position and orientation) information of the robot must be obtained as an important sensory feedback. Usually, a magnetic tracking method is used to provide the pose information. Due to the magnetic disturbance, a traditional magnetic tracking method cannot work simultaneously with the magnetic manipulation system. In this paper, a simultaneously tracking and navigation method is proposed to realize a closed-loop control of the magnetically manipulated untethered robot. The main approach is to conduct a multi-object tracking of the involved magnetic objects. With the proposed method, real-time pose information can be estimated during the manipulation, and both the tracking and manipulation are carried out by a magnetic manner. Therefore, the mobile navigation of the magnetically manipulated untethered robot can be achieved by using a pre-defined map. Experimental results verified the proposed method, and a mean position error of 1.2 mm for the passive magnet has been obtained.