The temperature and flow rate control of diffusing chamber is one of the key technologies in the production of poly-crystal silicon thin film. As there exist some modeling uncertainties and errors in the actual system, it is difficult to guarantee the chamber variable temperature conditions and the flow rate of diffusion gas being controlled within its targeted range in the rapid thermal processing (RTP). In this paper, the control applies the programmable logic controller (PLC) to configure control hardware system, proposes expert proportional integral derivative (PID) control method to regulate the gas flow rate and H∞ control strategy to attenuate chamber modeling uncertainties and disturbances, respectively, to steer the chamber rapid variable temperature very close to the expected product temperatures. Furthermore, it designs human-machine integrated user control interface (HMI) and achieves rapid and accurately control performances for user operating production. The designed control system are simulated and tested in the application, which demonstrates that the control method has strong robustness when the modeling uncertainties, errors, parameters perturbation and disturbances, the temperature and flow rate meet the requirements of precisely trajectory following.