This paper presents a study on the position tracking control of a robot system on the uncertain elastic base. The elastic bathe is a nonholonomic system but it can be changed into holonomic system, which is much easier to analyze, by modeling an elastic base as a virtual robot that has passive joints. Also, Jacobian operators, which represent the overall robot system including base movement, are defined and applied to the changed model. However, because base movements are not known, the exact Jacobian operators can＇t be estimated. The control algorithm proposed is that uses only Jacobians of a real robot as approximate Jacobian operators. Therefore the approximate Jacobian operators compensate the measured errors from external sensors. The proposed control strategy is evaluated by the simulation and experiment of a single-axis robot system on the elastic base.