Throughout the course of a flight mission, a range of aerodynamic conditions, including design-point conditions and off-design conditions, are encountered. As the bypass ratio increases and the fan-pressure ratio decreases to reduce the engine’s specific fuel consumption, the engine diameters increase, which results in an increase in the nacelle weight and overall drag. To reduce its weight and drag, a shorter nacelle with a length-to-diameter ratio $L/D = 0.35$ is investigated. In this study, an adaptive cokriging-based multi-objective optimisation method is applied to the design of a short aero-engine nacelle. Two nacelle performance metrics were employed as the objective functions for the optimisation routine. The cruise drag coefficient is evaluated under cruise conditions, whereas the intake pressure recovery is evaluated under takeoff conditions. The cokriging metamodel are refined using an effective infilling strategy, where high-fidelity samples are infilled via the modified Pareto fitness, and low-fidelity samples are infilled via the Pareto front. By combining parameterised geometry generation, automated mesh generation, numerical simulations, surrogate model construction, Pareto front exploration based on the non-dominated sorting genetic algorithm-II and sample infilling, an integrated multi-objective optimisation framework for short aero-engine nacelles is developed. Two-objective and three-objective test functions are used to validate the effectiveness of the proposed framework. After the optimisation process, a set of non-dominated nacelle designs is obtained with better aerodynamic performance than the original design, demonstrating the effectiveness of the optimisation framework. Compared with the kriging-based optimisation framework, the cokriging-based optimisation framework outperforms the single-fidelity method with a higher hypervolume value at the same number of iteration loops.