Winter irrigation is widely carried out to alleviate soil salinization in Northwest China. In recent years, the effects of irrigation amount and irrigation schedule on soil water and salt distribution and water use efficiency (WUE) during crop growth periods have been extensively studied, but the effects of winter irrigation on water use efficiency have been generally ignored. This work was conducted from November 2018 to October 2020 in two kinds of saline-alkali farmlands (mild saline-alkali farmland and moderate saline-alkali farmland) with five winter irrigation amounts (0, 150, 225, 300 and 375 mm). The results indicated that, during the winter irrigation period, the maximum moisture content layer in the soil becomes more shallow with the increase in the winter irrigation amount and the salinity of the soil. The salt return process mainly occurs during the late thawing period. After two years, for a winter irrigation amount of 150 mm to 375 mm, the change rate of soil salt in mild saline-alkali farmland decreased from −2.50% to −15.38% in the 0–100 cm profile, and that value in moderate saline-alkali farmland decreased from 12.22% to −16.85%. Compared with the non-winter irrigation treatment, the sprouting rate, survival rate, morphological index and cotton yield in the coming year are greater under the winter irrigation treatment. For mild saline-alkali farmland and moderate saline-alkali farmland, to keep soil desalinated, enhance cotton growth and save water resources, the recommended winter irrigation amounts are 225 mm and 300 mm, respectively. The research methods and results are of great significance for rationally evaluating the sustainable winter irrigation amount for cotton fields under mulched drip irrigation in different saline-alkali farmlands.