To reduce potential trauma to the intestine caused by the rigid shell while also optimising its progression efficiency, an elastomer coating was applied to a self-propelled capsule robot for small-bowel endoscopy. The robot is self-propelled by its periodically excited inner mass interacting with the main body of the capsule in the presence of intestinal resistance. This work explored the dynamic responses of the capsule with different elastomer coatings (i.e., different elastic moduli and thicknesses) in the lumen of the small intestine through a three-dimensional finite element analysis. The driving parameters of the robot, including the amplitude, frequency and duty cycle of a square-wave excitation, were further tested to reveal the dynamics of this soft robot. By analysing numerical results, the proposed finite element model can provide quantitative predictions on the contact pressure, resistance force and robot-intestine dynamics under different elastomer coatings. It was found that the softer the elastomer coating is, the lesser the contact pressure between the robot and the intestine, thus implying lesser trauma. The findings of this work can provide design guidelines and an evaluation means for robotic engineers who are developing soft medical robots for bowel examinations as well as clinical practitioners working on capsule endoscopy.