High complexity of modern civil aircraft system leads to a huge difficulty to its trouble-shooting. This paper firstly discussed the two main directions of improving the aircraft fault diagnosis capability, and then analysed the pain points encountered by the model-based troubleshooting method. For the pain points, the Colour Fuzzy Fault Petri Net (CFFPN) model was proposed. The basic principles of the model and the basic process of conducting forward and reverse reasoning diagnosis based on the model were illustrated. Then the application of reasoning process in system design integration and airline maintenance was expounded. Finally, a practical software prototype of the model was developed, and effectiveness of the method and model was demonstrated through applications in engineering practice.