Abstract Morphing aircraft can meet requirements of multi-mission during the whole flight due to changing the aerodynamic shape, so it is necessary to study its morphing rules along the trajectory. However, trajectory planning considering morphing variables requires a huge number of expensive CFD computations due to the morphing in view of aerodynamic performance. Under the given missions and trajectory, to alleviate computational cost and improve trajectory-planning efficiency for morphing aircraft, an offline optimization method is proposed based on Multi-Fidelity Kriging (MFK) modeling. The angle of attack, Mach number, sweep angle and axial position of the morphing wing are defined as variables for generating training data for building the MFK models, in which many inviscid aerodynamic solutions are used as low-fidelity data, while the less high-fidelity data are obtained by solving viscous flow. Then the built MFK models of the lift, drag and pressure centre at the different angles of attack and Mach numbers are used to predict the aerodynamic performance of the morphing aircraft, which keeps the optimal sweep angle and axial position of the wing during trajectory planning. Hence, the morphing rules can be correspondingly acquired along the trajectory, as well as keep the aircraft with the best aerodynamic performance during the whole task. The trajectory planning of a morphing aircraft was performed with the optimal aerodynamic performance based on the MFK models, built by only using 240 low-fidelity data and 110 high-fidelity data. The results indicate that a complex trajectory can take advantage of morphing rules in keeping good aerodynamic performance, and the proposed method is more efficient than trajectory optimization by reducing 86% of the computing time.