To investigate the effects of engineering operating parameters and storage structural characteristics on the performance of engineering-scale aquifer hydrogen storage, a three-dimensional domal aquifer hydrogen storage model incorporating capillary effects is established. The model is based on immiscible two-phase flow theory, coupling the flow of hydrogen and brine. Capillary pressure and relative permeability relationships are incorporated to describe two-phase seepage in porous media. Based on this model, simulation scenarios with varying injection rates, production rates, and storage steepness are designed. Multicycle injection-production simulations are conducted to systematically analyze hydrogen migration, gas-phase distribution, pressure evolution, and recovery efficiency variations. The results are as follows: (1) The injection rate primarily affects gas-phase distribution during the initial storage cycles: higher injection rates enhance viscous forces, producing pronounced viscous fingering at the gas front and reducing early-cycle recovery efficiency. As the injection-production cycles proceed, cushion gas forms and stabilizes, and the influence of injection rate on recovery efficiency markedly diminishes. (2) Compared with the injection rate, the production rate has a more persistent and substantial influence on storage performance: higher rates intensify formation-water encroachment, increase trapped residual gas, and cause earlier productivity decline, thereby reducing cyclic recovery efficiency. (3) storage structural steepness is an important controlling factor affecting aquifer hydrogen storage performance: greater steepness facilitates rapid upward hydrogen migration and accumulation toward the structural crest, promoting a continuous gas cap and improving single-cycle and cumulative recovery efficiencies. However, owing to the reduced effective pressure-bearing volume, steeply inclined storages exhibit larger pressure fluctuations during injection and production, imposing higher requirements on storage pressure management.