This paper establishes an agent-based simulation system of the carbon emissions trading in accordance with the complex feature of the trading process. This system analyzes the impact of the carbon quota allocation mechanism on emissions trading for three different aspects including the amount of emissions reduction, the economic effect on the emitters, and the emissions reduction cost. Based on the data of the carbon emissions of different industries in China, several simulations were made. The results indicate that the emissions trading policy can effectively reduce carbon emissions in a perfectly competitive market. Moreover, by comparing separate quota allocation mechanisms, we obtain the result that the scheme with a small extent quota decrease in a comprehensive allocation mechanism can minimize the unit carbon emission cost. Implementing this scheme can also achieve minimal effects of carbon emissions limitation on the economy on the basis that the environment is not destroyed. However, excessive quota decrease cannot promote the emitters to reduce emission. Taking into account that several developing countries have the dual task of limiting carbon emissions and developing the economy, it is necessary to adopt a comprehensive allocation mechanism of the carbon quota and increase the initial proportion of free allocation.