The tracking control based on output feedback for a category of flexible-joint robot (FJR) systems is investigated in this brief. Control performance of the systems is inevitably bearing the brunt of various unknown time-varying disturbances, which can be categorized to be matched and mismatched and generally cover internal parameter uncertainties, couplings, unmodelled dynamics, and external load or changing operating environments. To cope with these disturbances, the mismatched disturbances are first transferred to the matched ones by a flatness method, which eliminates the computational cost of estimating mismatched disturbances. Then, a generalized proportional integral observer (GPIO) is constructed to estimate the unavailable states and disturbances. By integrating the estimated disturbance and states provided by the GPIO, a novel dynamic sliding surface is constructed. Finally, a continuous sliding mode control (CSMC)-based output feedback control framework is further designed. The presented control strategy only requires link position information and is continuous, which can effectively reduce the chattering driven by the high-frequency switching item in the traditional SMC method. Asymptotic convergence of output tracking error is guaranteed by theoretical analysis under some mild conditions. Comparative tests on a two-link FJR verify the claimed control performance.