A thermally compensated frequency stabilization system is nonlinear with large time delay. Its control process is too complex to describe with the traditional model. As a result, the conventional PID algorithm designed by experiment has the disadvantages of difficulty in adjustment and control performance. This paper presents a new algorithm; model predict control (MPC) algorithm, which uses the Hammerstein model for forecasting the process output over a certain horizon in the future, optimizing the control in long-range predictive control strategy. The concept is implemented in a real industry scale single-chip-processor controlled thermally compensated frequency stabilization system. The result indicates that the algorithm is evvective. The laser tube reached a frequency stability of 6.7×10-9 in the sampling period of 10 s.