Green hydrogen has become the key to social low-carbon transformation and is fully linked to zero carbon emissions. The carbon emissions trading market is a policy tool used to control carbon emissions using a market-oriented mechanism. Building a modular carbon trading center for the hydrogen energy industry would greatly promote the meeting of climate targets. Based on this, a “green hydrogen market—national carbon trading market–electricity market” coupling mechanism is designed. Then, the “green hydrogen market—national carbon trading market–electricity market” mechanism is modeled and simulated using system dynamics. The results are as follows: First, coupling between the green hydrogen market, carbon trading market and electricity market can be realized through green hydrogen certification and carbon quota trading. It is found that the coupling model is feasible through simulation. Second, simulation of the basic scenario finds that multiple-market coupling can stimulate an increase in carbon price, the control of thermal power generation and an increase in green hydrogen production. Finally, the proportion of the green hydrogen certification, the elimination mechanism of outdated units and the quota auction mechanism will help to form a carbon pricing mechanism. This study enriches the green hydrogen trading model and establishes a multiple-market linkage mechanism.