Microwave irradiation (MI) is a leading-edge technology for increasing the permeability and production of coalbed methane (CBM) reservoirs. To study the characteristics of thermal response, pore-fracture structure and seepage behavior of coals under MI, a microwave heating device was operated to irradiate five different rank coal samples for 2 and 4 min. The variation of chemical structure has been explored using Fourier transform infrared spectroscopy (FTIR). The variation of pore fracture has been studied via low-field nuclear magnetic resonance (LF-NMR) and micro-computed tomography (μ-CT). Additionally, the pore distribution heterogeneity has been analyzed by multifractal dimension, an equivalent pore-fracture network model has been established by μ-CT, and the modification benefit of coal pore-fracture structure under MI has been revealed by simulation of absolute permeability. The results showed that the temperature of the coal samples reached 220−440 °C under MI for 4 min. The chemical structure of the coal samples did not change significantly. The P total , P free , connectivity, and D f increased, while the proportion of adsorption pores, P bound , and T 2c decreased under MI. The permeability significantly increased under MI, based on the single-phase water fluid flow simulation. The modification of coal pore fracture under MI was controlled by the physical and chemical structures of coal. The more developed the pore fracture, the better the modification effect under MI. The chemical structure of low-rank coal was more disordered, compared to high-rank coal, and the higher the thermal stress value generated under MI, the stronger the degree of pore-fracture damage. This study might provide some details for increasing fractures and permeability in coal reservoirs and increasing CBM production.