<p>To enhance the low-carbon operation capability of energy systems and promote the integration of renewable energy, a multi-energy collaborative optimization model based on electricity-carbon-green certificate market trading mechanisms are proposed. By establishing a generation right sharing platform, the study delves into the resource optimization allocation mechanism within the alliance to achieve carbon emission reduction, economical benefit optimization, and improved renewable energy accommodation. The model is solved using a mixed-integer programming approach, and the participation strategies and optimization processes of the multi-energy alliance in diverse markets are analyzed. The results indicate that the generation right sharing mechanism significantly enhances the overall benefits of the alliance, reduces system carbon emissions, and increases the integration of renewable energy. Meanwhile, the synergistic effects of heterogeneous energy sources, including wind power, photovoltaic power, hydropower, and thermal power, play a vital role in optimizing the alliance’s operational objectives. The proposed low-carbon operation model provides an effective decision-making reference for participants in diversified markets and offers theoretical support for the sustainable development of energy systems.</p>