An autonomous control system is developed for a shape-shifting robot "AMOEBA-I" to be possibly used in the urban terrain. Based on the sensors including GPS, electronic compass, inclinometer and encoder, the autonomous motions of AMOEBA-I are realized. The shape-shifting motion, navigation, obstacle-climbing motion, and obstacle avoidance are all autonomously performed in unstructured environments by the robot "AMOEBA-I". Experiments have been performed to validate the effectiveness of the developed autonomous control system.