In high reliability system, majority arbitration is a common means which can avoid the risk caused by single error. In order to ensure the accuracy of the judgment of the actuating equipment, the output of the processors must have ample synchronization. Meanwhile, there is no absolute dependence between the signals. A dynamic calibration method of de master-slave synchronization interrupt based on Zynq-7000 All Programmable SoC is designed. The processor’s instruction is issued when the trigger by synchronization interrupt, which can ensure the synchronization of next step. Through simulation and test, when the crystal oscillator accuracy≥50 ppm, the final millisecond interrupt can achieve sub microsecond synchronization accuracy.