In order to realize the reliability evaluation of the intelligent substation protection system, it is very important to establish an accurate reliability evaluation model of the protection system. In this paper, Weibull distribution is used to characterize the change of equipment failure rate over time when the equipment is aging. Combined with the planned maintenance behavior of the protection system, the improvement factor is used to characterize the reduction effect of planned maintenance on the equipment failure rate, establishing the reliability evaluation model of intelligent substation protection system with incompletely planned maintenance and the aging of the equipment. Taking the line protection system as an example, the reliability of the line protection system is evaluated by plotting the time-varying curve of the line protection system reliability and calculating the mean time between failure and planned maintenance cost of the line protection system. The results show that the proposed method can more accurately reflect the aging of equipment and the actual maintenance effect. This work is supported by National Natural Science Foundation of China (No. 51377137) and Science and Technology Project of State Grid Corporation of China (No. 52199916024N).