There are problems of high carbon emission in the process of coal mining and the lack of timely and effective use of associated energy such as that from a ventilation air meter, coal mine gas and mine gushing water. Thus a coal mine integrated energy system (CMIES) with low carbon and economic operation is proposed. First, to make full use of the associated energy in the mining area, a CMIES model including gas turbine, exhaust air oxidation power generation unit, water source heat pump and other equipment is built. Secondly, in order to reduce the carbon emissions, equipment such as photovoltaic, wind power, power-to-gas and hydrogen fuel cells are added to the CMIES. At the same time, stepwise carbon and green certificate trading mechanisms are introduced to constrain the system’s carbon emissions and stimulate the output of new energy equipment through the ‘dual mechanism’ model. Finally, the CPLEX commercial solver is used to solve the objective function with the minimum energy purchase, new energy equipment operation and carbon emission costs. The results show that the optimized CMIES carbon emissions are significantly reduced and the operating costs are greatly lowered.