Recently, the estimation of remaining useful life (RUL) for two-phase nonlinear degrading devices has shown rising momentum for ensuring their safe and reliable operation. The degradation processes of such systems are influenced by the temporal variability, unit-to-unit variability, and measurement variability jointly. However, current studies only consider these three sources of variability partially. To this end, this paper presents a two-phase nonlinear degradation model with three-source variability based on the nonlinear Wiener process. Then, the approximate analytical solution of the RUL with three-source variability is derived under the concept of the first passage time (FPT). For better implementation, the offline model parameter estimation is conducted by the maximum likelihood estimation (MLE), and the Bayesian rule in conjunction with the Kalman filtering (KF) algorithm are utilized for the online model updating. Finally, the effectiveness of the proposed approach is validated through a numerical example and a practical case study of the capacitor degradation data. The results show that it is necessary to incorporate three-source variability simultaneously into the RUL prediction of the two-phase nonlinear degrading systems.