Aiming to meet the low-carbon demands of power generation in the process of carbon peaking and carbon neutralization, this paper proposes an optimal PV-hydrogen zero carbon emission microgrid. The light–electricity–hydrogen coupling utilization mode is adopted. The hydrogen-based energy system replaces the carbon-based energy system to realize zero carbon emissions. Firstly, the mathematical models of photovoltaic, hydrogen and electric energy storage systems in a microgrid are built. Then, the optimal allocation model of the microgrid source storage capacity is established, and a scheduling strategy considering the minimum operational cost of energy storage equipment is proposed. The priority of equipment output is determined by comparing the operational costs of the hydrogen energy storage system and the electric energy storage system. Finally, the proposed scheme is compared with the scheduling scheme of the battery priority and the hydrogen energy system priority in an actual microgrid. It is verified that the scheme can ensure stable power-generating, zero carbon operation of a microgrid system while reducing the total annual power costs by 9.8% and 25.1%, respectively.