To solve the problem of online mistuning identification of bladed disks, this paper proposes a novel mistuning identification method based on proper orthogonal modes (POM-ID) and the response data. Firstly, the proposed method is analyzed by numerical simulation technology, and the influence of related parameters on the identification results is discussed. Compared with the traditional method, the effectiveness of the proposed method is verified. Secondly, the POM-ID method is applied to identify the mistuning parameters of an actual bladed disk based on the blade tip timing test data. Finally, the identification results of the rotating bladed disk are verified by using static test results, and the dynamic model of the bladed disk is updated. The accuracy of the updated model is confirmed by the aspects of natural frequency and vibration coupling effect. The results indicate that the natural frequency error of the modified model is less than 1%, and the vibration coupling law between blades is consistent with the test results. The mistuning identification method proposed in this paper is especially suitable for test data of the rotating bladed disk and is expected to be applicable for online dynamic updating of the bladed disk model.