The microstructure of oil shale plays a vital role in the seepage and production of shale oil and gas and can be modified by microwave irradiation. In this study, the experimental work aims to visualize and analyze the microstructure of oil shale under microwave heating with different heating parameters by traditional two‐dimensional (optical microscope and scanning electron microscope) and advanced three‐dimensional (micro‐CT) methods. Volumetric reconstructions of oil shale before and after microwave heating were completed to directly visualize the pore structure and fracture network of the samples. The similarities and differences between microwave heating and conventional heating were also investigated. Finally, based on the three‐dimensional CT data, the porosity and the degree of anisotropy of the samples were calculated. Traditional two‐dimensional imaging methods showed that microwave heating led to more pores and fractures due to the differential thermal stress caused by rapid heating, which differed from conventional heating. Porosity calculations based on the CT image data indicated that a long heating time and a high output power could lead to a large porosity value. Oil shale obtained by drilling horizontally into the bedding plane showed the largest porosity and lowest heterogeneity of pore distribution after heating and had a different fracture morphology. The results from this study are important for the exploitation of oil shale using microwave heating, and the application of these analytical techniques is useful for the evaluation of the flow behavior of transformation products.