This study proposes an optimum zero-carbon energy dominated fuel mix integrated with pumped hydro storage and green vehicles for a typical city to advance decarbonized operations by 2050 covering residential, commercial, industry and transport sectors. The flexible energy management strategy of the energy fuel and storage mix is proposed to integrate pumped hydro storage, battery vehicles and hydrogen vehicles to maintain power reliability and low-carbon transport. Multi-objective optimizations are conducted to determine optimum ratio composition of the energy fuel mix and sizing configurations of the pumped hydro storage, considering the trade-off between grid integration, energy cost and decarbonisation potentials. The research results show that the optimum energy fuel mix consists of 13% solar photovoltaics, 30% offshore wind power, 25% nuclear energy, 4% waste-to-energy and 28% natural gas. An additional 7% is sourced from natural gas to backup for the power mismatch, resulting in an energy capacity ratio of supply and demand at 1.07: 1. The hybrid pumped hydro and battery vehicle storage reduces the grid exchange energy of the mixed energy city by about 4041.36 GWh, lower by 40.89% than the case without storage. The levelized cost of energy of the optimum energy fuel mix for the decarbonized city is about 0.0846 US$/kWh. Obvious decarbonisation benefits can be achieved with the annual equivalent carbon emissions reduced by about 57.87% compared with the current local fuel mix. The flexible management and optimization model of developing the optimum zero-carbon energy dominated fuel mix integrated with pumped hydro storage and green vehicles provides a possible pathway towards carbon–neutral cities by 2050 covering the building, industry and transport sectors.