Gully Land Consolidation (GLC) is a proven method to create farmlands and increase crop yields in the Loess Hilly and Gully Region, China. However, GLC influences phreatic water transformation and might cause the farmlands water disasters, such as salinization and swamping. For exploring the influence of GLC on phreatic water transformation and mitigating disasters, a series of indoor experiments were conducted in the artificial rainfall hall. Then, we simulated the phreatic water transformation patterns under more conditions with HYDRUS-3D. Finally, an engineering demonstration in the field was performed to validate our research. The indoor experiments indicated that GLC could increase phreatic water outflow rate 4.39 times and phreatic water coefficient (PWC) 2.86 times with a considerable delay. After calibration and validation with experimental data, the HYDRUS-3D was used to simulate phreatic water transformation under more soil thickness and rainfall intensities. Accordingly, we summarized the relationship among PWC, rainfall intensities, and soil thickness, and therefore suggested a blind ditch system to alleviate farmlands disasters. Field application showed that a blind ditch system could avoid disasters with 3.2 times the phreatic water transformation rate compared to loess. Our research provides implications for sustainable land uses and management in the region with thick soil covers.