A two-stage electricity-hydrogen-ammonia or electricity-hydrogen-natural gas grid-connected energy system optimal scheduling model is proposed to address the many problems of the traditional integrated energy system. Firstly, a two-stage electric-hydrogen-ammonia and electric-hydrogen-gas equipment synergistic operation mechanism is established to flexibly coordinate water-hydrogen energy allocation. Second, the coupled equipment of carbon capture, utilisation and storage is introduced to construct the economic operation model of the system. Ultimately, the factual purpose of the system is to reduce economic costs. The results show that the integrated energy system with coupling equipment such as electricity-to-ammonia and electricity-to-gas has obvious optimisation effects in wind energy, solar energy consumption and low-carbon environmental protection, and the optimisation strategy of unit joint scheduling provides an effective guarantee for the system economy.