This paper presents a modified NSGA-II algorithm based on the spatial density (SD) operator, combined with computer graphics-based surface parameterisation methods and computational fluid dynamics (CFD) simulations. This was done to optimise the multi-objective aerodynamic design of a centrifugal impeller for a 100-kW vehicle-mounted fuel cell and improve the multi-conditions aerodynamic performance of the centrifugal impeller of the vehicle-mounted fuel cell (FC). The optimisation objectives are to maximise the isentropic efficiency of the rated and common operating conditions. The optimisation results showed that the efficiency of rated working conditions had an increase of 1.29%, mass flow increase of 8.8%, pressure ratio increase of 0.74% and comprehensive margin increase of 6.2%. The efficiency of common working conditions had an increase of 1.2%, mass flow increase of 9.1%, pressure ratio increase of 0.24% and comprehensive margin increase of 10%. The optimisation effect is obvious under the premise of satisfying the constraints, which proves the optimisation method’s engineering effectiveness and provides technical support and methodological research for the multi-objective aerodynamic design optimisation of centrifugal impellers for vehicle-mounted FCs.