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Winter wheat and cotton are the main crops grown on the North China Plain (NCP). Cotton is often transplanted after the winter wheat harvest to solve the competition for cultivated land between winter wheat and cotton, and to ensure that both crops can be harvested on the NCP. However, the root system of transplanted cotton is distorted due to the restrictions of the seedling aperture disk before transplanting. Therefore, the investigation of the deformed root distribution and water uptake in transplanted cotton is essential for simulating soil water movement under different irrigation methods. Thus, a field experiment and a simulation study were conducted during 2013–2015 to explore the deformed roots of transplanted cotton and soil water movement using border irrigation (BI) and surface drip irrigation (SDI). The results showed that SDI was conducive to root growth in the shallow root zone (0–30 cm), and that BI was conducive to root growth in the deeper root zone (below 30 cm). SDI is well suited for producing the optimal soil water distribution pattern for the deformed root system of transplanted cotton, and the root system was more developed under SDI than under BI. Comparisons between experimental data and model simulations showed that the HYDRUS-2D model described the soil water content (SWC) under different irrigation methods well, with root mean square errors (RMSEs) of 0.023 and 0.029 cm3 cm−3 and model efficiencies (EFs) of 0.68 and 0.59 for BI and SDI, respectively. Our findings will be very useful for designing an optimal irrigation plan for BI and SDI in transplanted cotton fields, and for promoting the wider use of this planting pattern for cotton transplantation.