Aiming at the low?carbon emission requirements and load demand characteristics of the integrated energy system, a comprehensive energy capacity allocation method considering the ladder carbon trading mechanism and hydrogen?blended natural gas is proposed. First of all, in order to alleviate the output volatility of wind and solar energy, a hydrogen energy system with hydrogen energy storage as the medium is established. Secondly, a hybrid hydrogen natural gas integrated energy system architecture comprising hydrogen energy storage and liquefied natural gas is created under the consideration of the substitution effect of hydrogen energy on natural gas. Then a ladder carbon trading mechanism is introduced to constrain the carbon emissions of the system. Finally, the capacity allocation is optimized with the annual total investment cost, including operating costs and annualized investment costs, as the objective function. The simulation results of the numerical example verify that the proposed model and strategy can reduce carbon emissions, total annual investment cost, and have important reference value for integreated energy allocation.