Under the background of low carbon electricity and energy interconnection, taking into account the difficulties in new energy consumption and other issues, based on the carbon emission trading (CET) mechanism, combined with the green certificate trading (GCT) mechanism, a regional integrated energy system (RIES) optimization method considering the green certificate-carbon quota mutual recognition mechanism is proposed. Firstly, the principles of carbon trading and green certificate trading are explored, and hydrogen fuel cell (HFC) equipment and hydrogen storage are introduced to optimize the electricity to gas process to further absorb new energy power generation. Secondly, carbon trading and green certificate trading are linked through mutual recognition of green certificate electricity and carbon emission quota, breaking the traditional barriers of carbon trading and green certificate trading. Finally, taking the minimum total cost of RIES as the objective function, an optimization model of RIES considering mutual recognition of green certificate and carbon quota is constructed. The simulation results show that the proposed method can effectively improve the economy of the system on the premise of ensuring a high energy utilization rate, and can improve the new energy consumption while reducing the carbon emissions of the system.