In order to reduce the fault tripping times of thermal power control system caused by logic design, access mode of protection signal, installation, commissioning, repair, maintenance, and so on, this paper investigated the hidden troubleshooting for the thermal control system and the prevention measures for the system reliability, based on the fault’s cause analysis, treatment experience and lessons for the thermal power control system, and the specification requirements of ‘the Reliability Deployment and Accident Prevention of Thermal Power Control System’. The prevention measures were suggested form the view of lightning protection, anti-interference, turbine supervisory instrumentation, logic reliability optimization, wiring and piping, technology and supervision management.