Underground hydrogen storage has been recognized as a key technology for storing enormous amounts of hydrogen, thus aiding in the industrial-scale application of a hydrogen economy. However, underground hydrogen storage is only poorly understood, which leads to high project risk. This research thus examined the effect of caprock availability and hydrogen injection rate on hydrogen recovery factor and hydrogen leakage rate to address some fundamental questions related to underground hydrogen storage. A three dimensional heterogeneous reservoir model was developed, and the impact of caprock and hydrogen injected rate on hydrogen underground storage efficiency were analysed with the model. The results indicate that both caprock and injection rate have an important impact on hydrogen leakage, and the quantities of trapped and recovered hydrogen. It is concluded that higher injection rate increases H ${}_2$ leakage when caprocks are absent. In addition, lower injection rates and caprock availability increases the amount of recovered hydrogen. This work therefore provided fundamental information regarding underground hydrogen storage project assessment, and supports the decarbonisation of the energy supply chain.