The moisture absorption and water conductivity of fabrics determine the thermal and moisture comfort of textiles and clothing. In this study, the water transfer law in cotton fabrics treated with a NaOH/urea system was investigated. The morphological changes and structural properties of the cotton fabrics before and after treatment were analyzed using scanning electron microscopy, Fourier transform infrared spectroscopy, and X-ray diffraction. Additionally, the relationship between the gaseous and liquid water transfer performance and the fiber morphology and structure was studied. The results indicate that after the NaOH/urea treatment, the surface of the cotton fibers gradually became rougher, and the fibers swelled slightly along the cross-sectional direction. With an increase in treatment time, the axial twist of the fibers decreased, and a trend of dissolution was observed. However, after 5 min of treatment, the cotton fabric tended to adhere to the partially dissolved fibers at the junction of the warp and weft yarns. Although the chemical structure of the cotton fibers did not show significant changes after the treatment, their crystallinity gradually decreased. Following treatment, the air permeability and moisture permeability of the fabric increased, while the wicking height and water retention rate initially increased and then decreased, resulting in an interesting pattern of change. The NaOH/urea treatment also increased the dyeability of the cotton fabrics, and the fastness to rubbing and washing of the fabrics reached grades ≥ 3. Prolonged NaOH/urea treatment enhanced the breaking strength of the cotton fabrics. The establishment of the entropy weight-TOPSIS method to evaluate the moisture transfer performance of fabrics treated with the NaOH/urea system has theoretical significance for the comprehensive analysis of cotton fabrics treated with NaOH/urea and related product development. This study provides a new basis for the comprehensive analysis and evaluation of the water transfer and moisture comfort performance of the fabrics, further advancing the application of NaOH/urea treatment to cotton fabrics, which has promising prospects for the future.