Personalized medicine is a hot topic to develop a medical procedure for healthcare. Motivated by molecular dynamics simulation-based personalized medicine, we propose a novel numerical simulation-based personalized diagnosis methodology and explain the fundamental procedures. As an example, a personalized fault diagnosis method is developed using the finite element method (FEM), wavelet packet transform (WPT) and support vector machine (SVM) to detect faults in a shaft. The shaft unbalance, misalignment, rub-impact and the combination of rub-impact and unbalance are investigated using the present method. The method includes three steps. In the first step, Theil's inequality coefficient (TIC)-based FE model updating technique is employed to determine the boundary conditions, and the fault-induced FE model of the faulty shaft is constructed. Further, the vibration signals of the faulty shaft are obtained using numerical simulation. In the second step, WPT is employed to decompose the vibration signal into several signal components. Specific time-domain feature parameters of all of the signal components are calculated to generate the training samples to train the SVM. Finally, the measured vibration signal and its components decomposed by WPT serve as a test sample to the trained SVM. The fault types are finally determined. In the simulation of a simple shaft, the classification accuracy rates of unbalance, misalignment, rub-impact and the combination of rub-impact and unbalance are 93%, 95%, 89% and 91%, respectively, whereas in the experimental investigations, these decreased to 82%, 87%, 73% and 79%. In order to increase the fault diagnosis precision and general applicability, further works are continuously improving the personalized diagnosis methodology and the corresponding specific methods.