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Multivariable stochastic degradation system (MSDS) is quite common in industries such as blast furnace ironmaking, vehicle transportation, and aerospace manufacturing. Large‐scale complex equipments may be affected by multiple factors, resulting in not just a single deteriorating performance characteristic. It is difficult to handle unknown failure structures of practical systems by using traditional univariate degradation modeling methods. A novel health index (HI) is constructed to quantitatively analyze the health state for the overall system. Considering the interaction between internal reactions and external environments, the fractional Brownian motion (FBM), a typical non‐Markovian diffusion process, is added for the purpose of reflecting stochastic uncertainties and memory effects. Based on the wavelet estimators and the maximum likelihood estimation (MLE) algorithm, multi‐sensor observations of degradation variables are analyzed simultaneously to identify model parameters. A closed‐form distribution of system‐level remaining useful life (RUL) is obtained with a mild two‐layer approximation. Relevant case studies are then handled that adequately demonstrate the effectiveness and the practical utility of the proposed method. [ABSTRACT FROM AUTHOR]