The position based feedback control system is proposed in order to improve the locomotive performance of the paddling based capsular microrobot moving in gastrointestinal (GI) tracts. The miniaturized optical encoder is designed and fabricated for the positional feedback of the mobile in the microrobot, which results in the precise positioning with the resolution of 0.1 mm. Moreover, the stroke of the mobile is optimized to increase the forwarding velocity of the microrobot. The control performance is verified by comparing the targeted displacement with the measured one under various loading conditions. The velocity of the microrobot is evaluated according to the various strokes and driving voltages under visco-elastically deformable and rare deformable conditions. The control system works properly with high resolution and accuracy and the velocity of the microrobot is maximized under the optimized stroke. In the in-vitro test, the velocity of the microrobot controlled by the position based feedback is increased by 73% when the optimized stroke is applied, compared with the velocity by the time based control.