A multi-objective optimization strategy to find optimal designs of composite multi-rim flywheel rotors is presented. Flywheel energy storage systems have been expanding into applications such as rail and automotive transportation, where the construction volume is limited. Common flywheel rotor optimization approaches for these applications are single-objective, aiming to increase the stored energy or stored energy density. The proposed multi-objective optimization offers more information for decision-makers optimizing three objectives separately: stored energy, cost and productivity. A novel approach to model the manufacturing of multi-rim composite rotors facilitates the consideration of manufacturing cost and time within the optimization. An analytical stress calculation for multi-rim rotors is used, which also takes interference fits and residual stresses into account. Constrained by a failure prediction based on the Maximum Strength, Maximum Strain and Tsai-Wu criterion, the discrete and nonlinear optimization was solved. A hybrid optimization strategy is presented that combines a genetic algorithm with a local improvement executed by a sequential quadratic program. The problem was solved for two rotor geometries used for light rail transit applications showing similar design results as in industry.