In view of the limitation of the conventional coal seam fracturing method, an ultrasonic stimulation method was proposed. Utilizing the combined effects of ultrasonic cavitation, mechanical vibration, and thermal conditions, the coal will form a network of intertwined cracks, and the gas will desorb and flow more easily. Current research on the changes of coal molecular and pore structure under ultrasonic stimulation is not in-depth. In this paper, the coal samples were treated by ultrasonic stimulation at 30 kHz frequency, and the changes of temperature, molecular structure, and pore structure of different scales were captured by combining a temperature acquisition unit, an infrared spectrometer, a stereoscopic microscope, a low-field nuclear magnetic resonance apparatus, and a three-dimensional X-ray microscope. The main conclusions are as follows: The temperature rise of coal during ultrasonic stimulation can be divided into three stages, namely, rapid rise, slow rise, and fluctuating rise. Also, the maximum temperature within 1 h can reach 263.9 °C. The oxygencontaining functional groups were decomposed and removed under ultrasonic stimulation, thus reducing the methane adsorption capacity of coal. The main fractures parallel to the bedding direction and the secondary branch fractures perpendicular to the bedding direction were produced. Furthermore, the primary and secondary fractures were penetrated, and the surface porosity increased to 3.93% after 3 h of treatment. Ultrasonic stimulation had little effect on the micropores and transition pores, but it increased the mesopores, macropores, and fractures. The effective porosity and free fluid proportion increased significantly with the increase in ultrasonic processing time by 43.86 and 31.30%, respectively. After ultrasonic stimulation, the scanned pore-fracture network model was highly connected and showed an ordered network and cross-linking, thus providing space for gas desorption and seepage.