A programmable logic controller based digital reactor protection system with an independent double structure redundancy per a channel and a method thereof are provided to improve stability and reliability of a nuclear power plant so as to maintain the nuclear power plant in a safety state and to prevent radioactive rays and radioactive materials from being leaked to the outside. A programmable logic controller based digital reactor protection system with an independent double structure redundancy per a channel includes four channels(200) of a redundancy structure which operates independently. Each channel includes a first group and a second group. The first group includes a first bistable processor(201a) among double bistable processors and a first coincidence processor(202a) among double coincidence processors. The second group includes a second bistable processor(201b) among the dual bistable processors and a second coincidence processor(202b) among the dual coincidence processors. The first and second bistable processors generate trip signals by comparing input signals with a predetermined stored trip set value on the basis of a plurality of sensing signals indicating states of reactor systems. The first and second coincidence processors generate a final trip signal by performing 2/4 logic compounding of the trip signals outputted from the bistable processors of a corresponding group among the four channels. A reactor is stopped by driving a reactor trip breaker or engineered safety features are operated by driving an engineered safety features-component control system according to the final trip signal by independent operation of the first and second groups of the redundancy structure in each channel.