The invention provides a nuclear power station reactor protection system and a safety control method therein, and relates to the field of a nuclear power station, for reducing the complexity of a protection system maintenance and regular test scheme. The protection system is provided with an emergency shutdown system dividing into N protection channels, wherein each protection channel obtains protection parameters from a signal preprocessing system and carries out a threshold comparison; a special driving system which is connected with the N protection channels, receives threshold comparison results, performs special driving logic processing according to the threshold comparison results and outputs first special driving instructions for driving an execution mechanism needing to be operated before a reactor reaches a controllable state after a nuclear power plant design reference accident takes place; and a safety automation system which is connected with the special driving system through a safety-grade ring network and generates first equipment-grade control instructions for controlling the execution mechanism needing to be operated when the state of the reactor is converted from the controllable state to a safe shutdown state after the nuclear power plant design reference accident takes place.