Autonomous locomotion in gastrointestinal (GI) tracts is achieved with a paddling-based capsule endoscope. For this, a miniaturized encoder module was developed utilizing a MEMS fabrication technology to monitor the position of paddles. The integrated encoder module yielded the high resolution of 0.0025 mm in the linear motion of the paddles. In addition, a PID control method was implemented on a DSP to control the stroke of the paddles accurately. As a result, the average accuracy and the standard deviation were measured to be 0.037 mm and 0.025 mm by a laser position sensor for the repetitive measurements. The locomotive performance was evaluated via ex-vivo tests according to various strokes in paddling. In an in-vivo experiment with a living pig, the locomotion speed was improved by 58% compared with the previous control method relying on a given timer value for reciprocation of the paddles. Finally, the integrated encoder module and the control system allow consistent paddling during locomotion even under loads in GI tract. It provides the autonomous locomotion without intervention in monitoring and controlling the capsule endoscope.