The assessment of socio-ecological systems can reflect the effects of nature, social economics, and human activities on the ecological environment, which is helpful to understand the context of complex social-ecological systems. Desert areas are ideal for socio-ecological system assessments because the land cover of deserts seriously influences the improvement of the local ecological environment and social economy. Yanchi County in the Ningxia Hui Autonomous Region is a typical desertification area where the ecological environment is very fragile. The government has implemented the Grain for Green Project and a prohibited-grazing policy to suppress and reverse desertification since 2000,and these ecological policies have positive effects on ecological restoration of desert areas. Therefore, it is very important to control desertification and maintain the normal function of local social-ecological systems. In this paper, the social-ecological system disturbance in Yanchi County was analyzed to understand the changes of the local social-ecological system. The MODIS (Moderate resolution Imaging Spectrometer) normalized difference vegetation index (NDVI) data of the study region was applied to investigate the spatial distribution of the existing social-ecological system disturbance during 2000-2015. In addition, moving window computational algorithms were used to calculate social-ecological system disturbance intensity and connectivity at different spatial scales. The results showed that (1) the disturbance had different spatial distributions over different periods, and strong disturbances were mainly distributed in southern Yanchi County during 2000-2004, whereas strong disturbances were distributed in the northern and central areas during 2004-2008. Furthermore, strong disturbances were detected in three small areas: southeastern, central, and western Yanchi County during 2008-2012. Moreover, the proportion of strong disturbances in the North showed an increasing trend. Strong disturbances were mainly distributed in the north, mid-west, and northwest of the county during 2012-2015. (2) There was a significant difference of disturbance intensity and connectivity of social-ecological systems at multi-scale levels. The types of clusters changed with the increase in the study window: lower disturbance discrete types converted to lower disturbance concentration types, and higher disturbance concentration types converted to lower disturbance discrete types. (3) Overall, except in some small areas, the disturbance intensity and connectivity of social-ecological systems were generally not large in most regions of Yanchi County. However, the desertification management is still insufficient, and the government should implement additional active policies to control desertification in the future.