The transient proper orthogonal decomposition (TPOD) method is applied for order reduction in the rotor-bearing system with the coupling faults in this paper. A 24 degrees of freedom (DOFs) rotor model supported by a pair of sliding bearings with both crack and rub-impact faults is established by the discrete modeling method. The complexity of dynamic behaviors of the rotor system with the coupling faults is discussed via the comparison of the rotor system with the single fault (crack or rub-impact). The proper orthogonal mode (POM) energy method is proposed to confirm the DOF number of the reduced model. The TPOD method is used in the coupling faults system to obtain the optimal order reduction model based on the POM energy. The efficiency of the order reduction method is verified by comparing the bifurcation behaviors between the original and the reduced system. The TPOD method provides the optimal order reduction model to study the non-linear dynamic characteristics of the complex rotor system with the coupling faults.