This paper studies a safe model predictive control (MPC)-based disturbance rejection control for a broad range of uncertain nonlinear systems subject to complex state safety constraints. The system under study is composed of a nominal model and an uncertain term that encapsulates modeling uncertainty, control mismatch, and external disturbances. In order to estimate the system state and total uncertainty, an extended state observer (ESO) is first designed. Utilizing the output of the ESO, the control compensates for the total uncertainty in real time and concurrently implements a control barrier function (CBF)-based MPC for the compensated system. The proposed control framework guarantees both safety and disturbance rejection. Compared to the baseline algorithm CBF-MPC, the proposed method significantly enhances system stability with a smaller root mean square (RMS) error of the system state from the equilibrium point. Rigorous theoretical analysis and simulation experiments are provided to validate the effectiveness of the proposed scheme.