In view of the magnetically actuated capsule robot applications in diagnoses of human stomach disease, the challenges that are associated with degrees-of-freedom (DOF), environmental adaptability, and the size of the entire system must be addressed. In this study, a new electromagnetic coil system that is based on adaptive magnetic levitation is presented; it is mainly composed of an independent orientation control electromagnetic coil and a magnetic levitation control electromagnetic coil. The system is designed to perform motion control of the capsule, including 3-DOF levitating translational motion control, and pitch and yaw motion control in levitation. In this manner, it compensates for the lack of previous magnetic levitation systems that were based on electromagnetic coils for the control of the tilt angle of the capsule. With torque-based actuation control, the tilt angle of the capsule can be controlled continuously with an angle increment of no more than 2 <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$^{\circ}$</tex-math> </inline-formula> (within 30 <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$^{\circ}$</tex-math> </inline-formula> ) during levitation. The capsule under the magnetic levitation control, which is based on the fuzzy proportional-integral -derivative controller, can maintain the stability of levitation; the error between the actual capsule position and the required position did not exceed 0.1 mm when the capsule was out of water or completely immersed in it. Moreover, the experiment of the capsule levitating from air to water further verifies the adaptability of the system with regard to the environment; this provides a new examination method for capsule endoscopy. <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Note to Practitioners</i> —This work is caused by the motion manipulation problem of a magnetically driven capsule robot. Most of the existing magnetically driven capsule robots use a rolling or sliding method that fits tightly against the stomach wall, and these forms of motion make it possible to risk missing diagnoses in the examination of gastric diseases, and the maneuverability limits its further application. This paper proposes an adaptive control strategy for a magnetically driven capsule robot based on magnetic levitation motion. It allows the magnetically driven capsule robot to levitate to any position in the stomach for photography and observation without external mechanical support, and this levitation motion is sufficiently stable. In addition, the proposed capsule robot has independent orientation and position control, which has the potential to achieve automated inspection.