Understanding the development of desiccation micro-cracks provides microscale insight into wetting-drying (W-D)-induced deterioration in soil hydro-mechanical behaviour. So far, the effect of fine particle migration on desiccation micro-cracks in intact loess with different clay contents during W-D remains unclear. In this study, an environmental scanning electron microscope (ESEM) was used to investigate how clay content influences fine particle migration and desiccation micro-cracks in intact loess during W-D. Results show that intact loess with higher clay content contains more clay connector assemblages and is more prone to fine particle migration during W-D. Migrated fine particles accumulate in macro-pores after drying and result in two types of desiccation micro-cracks. Type-Ⅰ and -II develop within the clay matrix and along the clay-coarse particle interface, respectively. However, only Type-II was observed in intact loess with lower clay content. This may be attributed to the limited amount of migrated fine particles, which is insufficient to infill macro-pores and instead accumulates in micro-pores, resulting in Type-II cracks. These observations offer a microscale explanation for the increased susceptibility to hydro-mechanical deterioration caused by W-D cycles in intact loess with higher clay content.