Facing the unfavorable situation of double restriction of water quantity and quality, China has put forward the new concept of ecological priority and green development, and at the same time has made it clear to adopt the market-oriented trading mechanism to control the water environment pollution. However, there are many shackles in the current market-oriented trading mechanism, and the effectiveness of policies on individual trading of emission rights cannot be judged. Therefore, based on the analysis of the real pollution control dilemma, the concept of water emission trading under the total amount control is introduced, and the trading logic of the multi-agent emission trading system is expounded. At the same time, a simulation model of the emission trading system is built based on the multi-agent system to simulate the dynamic game relationship between the government's policy regulation and the emission enterprises in the process of emission trading. The simulation results show that the emission trading system under the total amount control can effectively encourage and punish the emission subject, and guide the emission enterprises to actively reduce emissions. The results also show that in the free competition market with weak regulation, the traders of water emission rights tend to collude against the rules and conceal the real price. However, when the government carries out strong control and effective supervision, and the superior government departments can take effective supervision over the subordinate departments, the water emission rights traders can reduce the phenomenon of violation and collusion.