Vertical joints are a key characteristic of loess, contributing to its strong anisotropies. This factor must be taken into consideration in engineering activities. The development mechanism of vertical joints in loess at great depths under the influence of dry-wet cycles was investigated, focusing on a highway tunnel passing through a loess irrigation area. The appropriate method was also explored for calculating this phenomenon. Through a comprehensive analysis of diffraction patterns and scanning electron microscopy, it was proposed that soluble salts in the loess play a key role in cementation. A significant amount of soluble salts dissolved in water and migrated downward during dry-wet cycles, disrupting the cementation of the loess. This results in a shift from point-to-point contact between soil particles to point-to-surface or surface-to-surface contact. Additionally, the recrystallization after migration leads to the development and expansion of fine pores in the loess. The continued expansion of the joint fracture volume also creates a pathway for further downward penetration of the water flow. This cyclical interaction between loess and water will facilitate the development of joint fractures at greater depths. The surface cracks and sinkholes in underground engineering activities carried out in similar strata are the visible signs of the progressive development of internal cracks in loess from the subsurface to the surface. The utilization of random joint mesh DNF in finite element software to convert joints into discrete, planar, and finite-size elements is a viable approach for representing the anisotropy of loess in calculations. It also introduces a new concept for the equivalent treatment of discontinuous problems using the continuous mechanics method.