Eco-migrant village is a special type of village with the dual significance of poverty alleviation and ecological protection, as well as the indispensable and crucial object for rural revitalization. The spatial deprivation (SD), which resulted from the process of spatial reconstruction, is a new problem emerging in the course of eco-migrant villages revitalization and sustainable development. In order to explore the rule of the SD, this paper constructs a spatial deprivation index (SDI) system with income and employment, education and training, social life, living environment and accessibility of public services as the main contents, based on the data of 70 eco-migrant villages (EMV) of Ningxia in 2017, calculates EMVs' SDI value, and detects the impact factors by geographical weighted regression and GeoDetector. The results show that: (1) the overall level of SD of EMVs is low, but the total index means is 0.023 higher than that of non-EMVs. (2) The spatial and temporal variations of EMVs' SDI are obvious, presenting a time trend of "low - rise - decline" and a spatial distribution pattern of "the lowest in the north - the highest in the middle - the second highest in the south". (3) Ethnic composition, terrain and landform, migration period, essential resources and economic zone are critical factors affecting the SD of EMVs, in which the first three have explanatory capacity of the total SDI, being 22.4%, 10.6% and 14.0%, respectively. SD measurement provides a new objective basis for evaluating production and life of eco-migrants, adjusting and refining policies, so that relevant departments can optimize and reallocate the spatial resources of EMVs to increase their ability and opportunities, and promote the overall revitalization of EMVs.