As an important driving force for economic development and social progress, women have become an important subject of well-being research. Human well-being is the state of physical and mental health as well as material affluence and includes a variety of factors, such as wealth, education, health, safety, amenities, way of life, and happiness. Based on the established research framework of the Women’s Development Index (WDI) in Northwest China, this paper first measured the objective well-being level of women in Shaanxi, Gansu, Qinghai, Ningxia, and Xinjiang from 2003 to 2020 under the influence of ecological factors. In addition, spatial disaggregation and comparative analyses of the spatial imbalance of women’s well-being in Northwest China were carried out using the Theil index and Dagum Gini coefficient. The results show that (1) the WDI in ecologically vulnerable areas in Northwest China increased from 0.525 in 2003 to 0.690 in 2020, indicating an overall increase in well-being. (2) The WDI in the five provinces gradually increased with fluctuations. Among them, Shaanxi always remained in first place in terms of the WDI. (3) From 2003 to 2020, the spatial imbalance of women’s well-being as measured according to the WDI in Northwest China first increased and then decreased. However, the gap in women’s well-being in Northwest China was smaller than the economic gap. (4) From 2003 to 2020, the well-being gap measured by the WDI among the 10 groups of provinces in Northwest China gradually decreased, and the development gap between the provinces and Shaanxi was the largest.