Recently, a variety of positioning and tracking methods have been proposed for capsule robots moving in the gastrointestinal (GI) tract to provide real-time unobstructed spatial pose results. However, the current absolute position-based result cannot match the GI structure due to its unstructured environment. To overcome this disadvantage and provide a proper position description method to match the GI tract, we here present a relative position estimation method for tracking the capsule robot, which uses the moving distance of the robot along the GI tract to indicate the position result. The procedure of the proposed method is as follows: firstly, the absolute position results of the capsule robot are obtained with the magnetic tracking method; then, the moving status of the robot along the GI tract is determined according to the moving direction; and finally, the movement trajectory of the capsule robot is fitted with the Bézier curve, where the moving distance can then be evaluated using the integral method. Compared to state-of-the-art capsule tracking methods, the proposed method can directly help to guide medical instruments by providing physicians the insertion distance in patients’ bodies, which cannot be done based on absolute position results. Moreover, as relative distance information was used, no reference tracking objects needed to be mounted onto the human body. The experimental results prove that the proposed method achieves a good distance estimation of the capsule robot moving in the simulation platform.