Compared to traditional, static-based flywheel systems, vehicle-mounted magnetic suspension flywheels face more complex operating conditions, and existing control strategies usually regard disturbances in vehicles under different operating conditions to be the same problem. Therefore, it is necessary to determine the interference from complex operating conditions and reasonably distinguish among them under different operating conditions to provide flywheel systems with strong stability (the rotor offset was less than 0.025 mm). Thus, this paper proposes a high-stability control strategy for flywheels based on the classification of vehicle-driving conditions and designs its control strategy by taking the vehicle-mounted magnetic suspension flywheel with a virtual inertia spindle as an example. First, according to the different vehicle working conditions and the varying interference intensities affecting the flywheel system, the working mode is divided into four modes. Considering the obvious differences in each working mode, it is proposed to use BP neural network optimization based on the simulated annealing algorithm (SA-BPNN) to determine the flywheel’s working condition. A relatively simple neural network can improve the response speed of the whole system. It also has a good effect. Secondly, it is proposed to use deep learning models based on convolutional neural networks, long short-term memory networks and attention mechanisms (CNN+LSTM+ATTENTION) to train the corresponding control parameters under each working condition to judge and predict the control parameters under different working conditions. Three evaluation parameters are used to evaluate the training results, and all achieved good results. Finally, the classification of working conditions and performance tests are carried out. The experimental results show the effectiveness and superiority of the proposed control strategy.