For the purpose of realizing the noninvasive exploration of gastrointestinal tract, a novel magnetic propulsion system is proposed, which includes a patient support, a magnet assembly with two groups of permanent magnets positioned oppositely, and a magnet support. The proposed approach exploits permanent magnet and coupling movement of multi-axis components to generate quasi-static magnetic field for controlling the position, orientation, and movement of a self-propelled robotic endoscope in the gastrointestinal tract. By driving the five coupling axes, the proposed magnetic propulsion system is capable of steering the capsule endoscope through the intestinal tract in multi-directions of 2D space. Experiments in simulated intestinal tract are conducted to demonstrate controlled translation, rotation, and rototranslation of capsule endoscope. Finite Element Method is used to analyze navigation system’s mechanical properties and the distributions of magnetic field. The proposed technique has great potential of enabling the application of controlled magnetic navigation in the field of capsule endoscopy.