As hydraulic fracturing as a means to enhance coal bed methane was banned in some countries due to possible negative environmental impacts, the microwave heating was proposed as an alternative approach to enhance coal permeability and thus gas productivity. One of the mechanisms on improving coal permeability using microwave irradiation is that thermal stress caused by microwave heating generates fractures. To study the influence of microwave settings to the heating effect of coal samples, a coupled mathematical model for electromagnetic, heat and mass transfer in the process of microwave heating is proposed and is numerically implemented using a finite element method. This coupled model for microwave heating have considered heat and mass transfer, and is validated by comparison with experimental results. Then it is used to simulate the influence of frequency, power and moisture capacity on microwave heating. The simulation results show that microwave heating of coal is highly sensitive to excitation frequency. Frequencies around 3.45 GHz contribute to significant thermal heterogeneity. With the same energy input, different powers do not influence the overall heating effect, but higher powers cause greater thermal heterogeneity. Moisture capacity also has great effect on microwave heating and thermal distribution pattern. Under 2.45 GHz and 1.0 kW, the coal sample with moisture capacity of 5% has the best microwave heating effect.