The adaptive tracking problem for uncertain flexible joint robot system is studied in this paper. By utilizing the adaptive backstepping method, an adaptive controller is constructed at the beginning. By utilizing the modified adaptive dynamic surface control technique, a new adaptive controller is presented afterwards to avoid the overparametrization problem and the explosion of complexity problem existing in the adaptive backstepping method. All the signals of the closed-loop system are rendered globally/semi-globally uniformly ultimately bounded, and the tracking error can be made arbitrarily small by tuning the designed parameters. A simulation example is given to show the validity of the control algorithm. The adaptive tracking problem for uncertain flexible joint robot system is studied in this paper. By utilizing the adaptive backstepping method, an adaptive controller is constructed at the beginning. By utilizing the modified adaptive dynamic surface control technique, a new adaptive controller is presented afterwards to avoid the overparametrization problem and the explosion of complexity problem existing in the adaptive backstepping method. All the signals of the closed-loop system are rendered globally / semi-pivor uniform ultimately bounded, and the tracking error can be made arbitrarily small by tuning the designed parameters. A simulation example is given to show the validity of the control algorithm.