Aiming at digital relay protection system, a novel hidden failure Markov reliability model is presented for a single main protection and double main protection systems according to hidden failure and protection function under Condition-Based Maintenance (CBM) circumstance and reliability indices such as probability of protection system hidden failure state are calculated. Impacts of different parameters (containing impacts of human errors) to hidden failure state probability and the optimal measures to improve reliability by variable parameter method are also analyzed. It’s demonstrated here that: Compared to a single main protection, double main protection system has an increased hidden failure probability, thus the real good state probability decreases, two main protections’ reliability must be improved at the same time, so configuration of the whole protection system for the component being protected can’t be complicated. Through improving means of on-line self-checking and monitoring system in digital protection system and human reliability, the real application of CBM can decrease hidden failure state probability. Only through this way can we assure that the protection systems work in good state. It has a certain reference value to protection system reliability engineering.