This paper presents the architecture of the reactor protection system (RPS) in a nuclear integrated safety system (NISS) and describes the evaluation and analysis of reliability for NISS-RPS using the Markov model. NISS-RPS has four-channel redundancy like existing digital RPSs. However, a channel is configured based on triple modular redundancy and can be reconfigured on detecting faults. To analyze and evaluate the reliability of NISS-RPS, the Markov model for NISS-RPS and RPSs that are in operation or under construction in Korea were developed. Their reliability was evaluated and analyzed using the models. From the reliability analyses for NISS-RPS, it was observed that the failure rate of each module in NISS-RPS should be <2 × 10−5/hour, and the mean time to failure (MTTF) is ∼20 000 hours, which is two times better than the MTTF requirement of 10 000 hours. The MTTF average increase rate, which depends on the fault coverage factor (FCF) increment, ΔMTTF/ΔFCF, is 1850 hours/0.1. The results of comparison with other RPSs show that the reliability of NISS-RPS is at least 1.5 times better than that of the other three types of RPS architecture, and the MTTF is at least 14 months longer than that of the other types.