Soil hydrology seriously affects the prevention of desertification in karst areas. However, water infiltration in the different soil layers of secondary forests and artificial forests in karst areas remains uncertain. This lack of clarity is also the factor that constrains local vegetation restoration. Therefore, monitoring and simulating the priority transport of soil moisture will help us understand the shallow soil moisture transport patterns after artificial vegetation restoration in the local area, providing a reference for more scientific restoration of the ecological environment and enhancement of carbon storage in karst areas. The integration of soil physical property assessments, computed tomography (CT) scanning, dye tracing studies, and HYDRUS-2D modeling was utilized to evaluate and contrast the attributes of soil macropores and the phenomenon of preferential flow across various forestland categories. This approach allowed for a comprehensive analysis of how the soil structure and water movement are influenced by different forest ecosystems and infiltration head simulations (5 mm, 15 mm, 35 mm, and 55 mm) to elucidate the dynamics of water movement across diverse soil types within karst regions, to identify the causes of water leakage due to preferential flow in secondary forests, and to understand the mechanisms of water conservation and reduction in artificial forests adopting a multifaceted approach. This study demonstrated that (1) the soil hydrological capacity of a plantation forest was 20% higher than a natural forest, which may be promoted by the clay content and distribution. (2) Afforestation-enhanced soils in karst regions demonstrate a significant capacity to mitigate the loss of clay particles during episodes of preferential flow and then improve the soil erosion resistance by about 5 times, which can effectively control desertification in karst area. (3) The uniform distribution of macropores in plantation forest soil was conducive to prevent water leakage more effectively than the secondary forest but was incapable of hindering the occurrence of preferential flow. The secondary forest had a very developed preferential flow phenomenon, and soil clay deposition occurred with an increase in depth. (4) Moreover, the results for preferential flow showed that the matrix flow depth did not increase with the increase in water quantity. Short-term and high-intensity heavy rainfall events facilitated the occurrence of preferential flow. Infiltration along the horizontal and vertical directions occurred simultaneously. These results could facilitate a further understanding of the contribution of the plantation to soil amelioration and the prevention of desertification in karst areas, and provide some suggestions for the sustainable development of forestry in karst areas where plantation restoration is an important ingredient.