The control system, as a safety-critical system in nuclear energy equipment, often needs to operate without human intervention for a long time in actual engineering. It demands extremely high levels of automation and operational reliability. The highly robust signal voting algorithm can ensure that the control system can automatically respond and return to normal operation when it encounters a fault or abnormal situation. At present, the signal voting algorithm commonly used in nuclear energy control system is threshold detection method. This kind of method is simple in structure and easy to understand, but its control accuracy, reliability and automation are not good. Therefore, based on the design of the nuclear energy control system under the condition of long period unmanned operation, this paper proposes a multi-level voting algorithm for the redundant signal of the nuclear energy control system based on voting mechanism to meet the high reliability and automation requirements of the system. The first-level monitoring algorithm determines the signal fault point, and on this basis, the second-level monitoring voting algorithm outputs the final voting value. In this paper, the signal sequence in the simulation process is intercepted, and the functions of the proposed algorithm such as output voting value, fault count, fault point elimination and recovery and output safety value are verified. At the same time, a variety of test signals are simulated for comparative verification. The results show that the proposed algorithm can effectively reduce the error probability of voting on step signals, ramp signals and sine signals. Its voting result is generally superior to that of traditional voting algorithms such as average and median, and the threshold operation result is better than that of traditional threshold detection methods. Finally, by discussing the time complexity of the algorithm and the average running time of the algorithm, the method is verified to meet the realtime requirements of the nuclear energy control system.