This paper focuses on the observer-based robust stabilization problem for a class of polynomial systems with norm-bounded time-varying uncertainties. The structural features of such systems guarantee the fulfilment of the separation principle between the reduced-order observer and the state feedback. The existence conditions of the observer-based robust stabilization controller are obtained by using Lyapunov stability theory. Furthermore, based on the polynomial sum of squares (SOS) theory, the above conditions are transformed into the corresponding SOS convex optimization constraints, for the avoidance of computing difficulties that exist widely in the control of non-linear systems. Finally, two numerical examples are given to illustrate the feasibility and effectiveness of the proposed approach.