Capsule medical robots with unique application advantages have broad prospects for gastrointestinal detection, targeted drug delivery, medical assistance, and other fields. However, due to the complexity of the gastrointestinal environment and the limitations of the space magnetic field, robust motion control of capsule robots is still a challenge. Using a permanent magnet (NdFeB) as a space magnetic source, a capsule robot manipulation instrument with an integrated motion intelligent control approach is proposed in this work. First of all, a steering fixture controlling a permanent magnet is designed, and a manipulation instrument capable of five degrees of motion freedom is built with low cost and high accuracy. Furthermore, an integrated motion control approach, consisting of a primary motion subsystem and an auxiliary motion subsystem, is presented, where the motion route of the capsule robot is planned. A parallel optimization strategy is adopted to improve the traditional Gray Wolf Optimization Algorithm, the improved version of which is utilized to tune the parameters of controllers. Finally, some experiments of the designed capsule robot are carried out in different planes and slopes, as well as simulated stomach and real pig stomach, respectively. The results show that the motion characteristics are continuous and stable, and the average position error is 4.2 mm, which meets the application requirements.