The tracking control problem for Flexible Joint Manipulator Control System (FJMCS) with unmeasurable states is addressed in this paper. Firstly, a High-Gain Observer (HGO) is constructed to estimate the unmeasurable states and the uncertainties. Then, a Dynamic Surface Control (DSC) scheme is developed by using the estimation of HGO. The newly proposed controller has two advantages over the existing methods: (A) a novel Spike Suppression Function (SSF) is developed to avoid the estimation spike problem in the existing HGO-based controllers. (B) Unlike the existing observer-based partial feedback control scheme that can only estimate the unmeasurable states, the proposed HGO can estimate both the unmeasurable states and uncertainties. The closed-loop system stability is proved by the Lyapunov theory. Simulation results demonstrate the effectiveness of the proposed controller.