In order to improve the accuracy and calculation efficiency of aeroengine rotor vibration reliability analysis, a time-varying rotor vibration reliability analysis method under the aeroengine operating state is proposed. Aiming at the highly nonlinear and strong coupling of factors affecting the reliability of aeroengine rotor vibration, an intelligent neural network modeling framework (short form-INNMF) is proposed. The proposed method is based on DEA, with QAR information as the analysis data, and four factors including engine working state, fuel/oil working state, aircraft flight state, and external conditions are considered to analyse the rotor vibration reliability. INNMF is based on the artificial neural network (ANN) algorithm through improved particle swarm optimization (PSO) algorithm and Bayesian Regularization (BR) optimization. Through the analysis of the rotor vibration reliability of the B737-800 aircraft during a flight mission from Beijing to Urumqi, the time-varying rotor vibration reliability was obtained, which verified the effectiveness and feasibility of the method. The comparison of INNMF, random forest (RF), and ANN shows that INNMF improves analysis accuracy and calculation efficiency. The proposed method and framework can provide useful references for aeroengine rotor vibration analysis, special treatment, maintenance, and design.