Due to the humidity difference between fine-grained clay and atmosphere environment, the complex crack network is formed, which is the main channel for water storage and migration and hence poses a potential threat to engineering construction. Therefore, the appropriate characterization of cracking behavior of fine-grained clay is of great significance for exploring its microphysical properties. To this end, this work took expansive soils as research object and a series of desiccation tests and X-ray computed tomography tests were conducted to investigate the shrinkage cracking behavior. The results indicate that a higher desiccation rate records a smaller shrinkage strain, but it aggravates the cracking on a much larger scale. Especially at high desiccation rates, two-dimensional crack ratio shows a significant fluctuation. Small cracks tend to turn into large ones during desiccation, and the increasing desiccation rate primarily exerts a significant effect on the cracks with equivalent radius more than 1000 µm. The expansive soil is dominated by horizontal cracks, and a low desiccation rate mainly promotes the connection between horizontal cracks, whereas high desiccation rates enhance the connectivity of oblique cracks, which exerts an adverse effect on soil slopes. Besides, the rise in desiccation rate leads to a wealth of micro-scale pores and throats occurring in the soil. The fine-grained clays at higher desiccation rates present larger pore and throat volume, more connected pores, and higher average coordination number, thus enhancing the connectivity between pore and pore. Permeability simulation results also confirm the positive correlation between connected crack ratio and hydraulic conductivity of the soil. In terms of engineering significance, narrowing down the difference in humidity between fine-grained clays and atmosphere is the most effective measure to constrain the extension of cracks.