To improve the endurance performance of long-endurance Unmanned Aerial Vehicles (UAVs), a smart morphing method to adjust the UAV and flight mode continuously during flight is proposed. Using this method as a starting point, a smart morphing long-endurance UAV design is conducted and the resulting improvement in the endurance performance studied. Firstly, the initial overall design of the smart morphing long-endurance UAV is carried out, then the morphing form is designed and various control parameters are selected. Secondly, based on multi-agent theory, an architecture for the smart morphing control system is built and the workflow of the smart morphing control system is planned. The morphing decision method is designed in detail based on the particle swarm optimisation algorithm. Finally, a simulation of the smart morphing approach in the climb and cruise stages is carried out to quantitatively verify the improvement in the endurance performance. The simulation results show that the smart morphing method can improve the cruise time by 4.1% with the same fuel consumption.