Due to the poor working conditions of an engine, its control system is prone to failure. If these faults cannot be treated in time, it will cause great loss of life and property. In order to improve the safety and reliability of an aero-engine, fault diagnosis, and optimization method of engine control system based on probabilistic neural network (PNN) and support vector machine (SVM) is proposed. Firstly, using the German 3 W piston engine as a control object, the fault diagnosis scheme is designed and introduced briefly. Then, the fault injection is performed to produce faults, and the data sample for engine fault diagnosis is established. Finally, the important parameters of PNN and SVM are optimized by particle swarm optimization (PSO), and the results are analyzed and compared. It shows that the engine fault diagnosis method based on PNN and SVM can effectively diagnose the common faults. Under the optimization of PSO, the accuracy of PNN and SVM results are significantly improved, the classification accuracy of PNN is up to 96.4%, and the accuracy of SVM is up to 98.8%, which improves the application of them in fault diagnosis technology of aero-piston engine control system.