The application of the proper orthogonal decomposition (POD) method to the vibration response of a cracked rotor system is investigated. The covariance matrices of the horizontal and vertical whirl amplitudes are formulated based on the numerical and experimental whirl response data for the considered cracked rotor system. Accordingly, the POD is directly applied to the obtained covariance matrices where the proper orthogonal values (POVs), and the proper orthogonal modes (POMs) are obtained for various crack depths, unbalance force vector angles, and rotational speeds. It is observed that both POVs and their corresponding POMs are highly sensitive to the appearance of the crack and the unbalance force angle direction in the neighborhoods of the critical rotational speeds. The sensitivity zones of the POVs and POMs to the crack propagation are found to be coinciding with the unstable zones found by the Floquet's theory of the considered cracked system.