The atomic clock′s frequency stability estimated by Allan variance will significantly deviate from its true value if anomalies occur. An uncorrelated differential robust estimation method based on Huber weight function was proposed. Firstly, a difference estimation model of Allan variance was established, and the computation complexity of noise identification and whitening introduced by correlated difference was analyzed on the basis of the statistical property of the clock difference sequence. In order to solve this problem, a construction model of uncorrelated difference sequence was established to avoid complex noise identification and whitening computation effectively. Based on this, the uncorrelated difference robust estimation method of Allan variance was derived, followed by a counteracted technique of error accumulation introduced by robust estimation. Finally, the integrated robust estimation solution was given, and its effectiveness was verified by experiment. The results show that the method has significance robustness for phase outliers and phase jumps, and the relative deviation introduced by anomalies can be reduced from almost 200% to less than 10%.