The energy base of urban settlements requires greater integration of renewable energy sources. This study presents a “hydrogen city” model with two cycles at the district and building levels. The main cycle comprises of hydrogen gas production, hydrogen storage, and a hydrogen distribution network. The electrolysis of water is based on surplus power from wind turbines and third-generation solar photovoltaic thermal panels. Hydrogen is then used in central fuel cells to meet the power demand of urban infrastructure. Hydrogen-enriched biogas that is generated from city wastes supplements this approach. The second cycle is the hydrogen flow in each low-exergy building that is connected to the hydrogen distribution network to supply domestic fuel cells. Make-up water for fuel cells includes treated wastewater to complete an energy-water nexus. The analyses are supported by exergy-based evaluation metrics. The Rational Exergy Management Efficiency of the hydrogen city model can reach 0.80, which is above the value of conventional district energy systems, and represents related advantages for CO2 emission reductions. The option of incorporating low-enthalpy geothermal energy resources at about 80 °C to support the model is evaluated. The hydrogen city model is applied to a new settlement area with an expected 200,000 inhabitants to find that the proposed model can enable a nearly net-zero exergy district status. The results have implications for settlements using hydrogen energy towards meeting net-zero targets.