The vegetation of the desert steppe plays an important role in preventing desertification, maintaining ecosystem stability, and constructing "Ecological Barrier" in Northwest China. However, most desert steppe ecosystems are very fragile and constantly face the risk of degradation. Yanchi County, located in eastern Ningxia province, is a typical desert steppe, and its vegetation dynamics in the past 13 years have been affected by both climate change and human activities. In order to explore the process and driving factors based on the Normalized Difference Vegetation Index (NDVI) derived from the Moderate-resolution Imaging Spectroradiometer (MODIS), we studied the vegetation dynamics in Yanchi County from 2000 to 2012. We used 296 scenes of MODIS NDVI data, all of these were converted to an Albers conical projection system and GeoTIF format by using the MODIS Reprojection Tool, and smoothed using the Savitzky-Golay filter to reconstruct a high-quality NDVI time-series data set. Annual and quarterly NDVI were synthesized using the Maximum Value Composite (MVC) method. In addition to MODIS NDVI data, the land use data of Yanchi in 2000 and 2011, meteorological data, and social statistical data were also used in this study. Multiple methods were used to analyze the vegetation dynamics in Yanchi County. A linear regression with an F test was used to analyze the trend of NDVI and its significance. The non-parametric Mann-Kendall test was used to detect the abrupt change in the long-term NDVI from 2000 to 2012. A non-linear and non-stationary signal analysis method, Empirical Mode Decomposition (EMD), was used to isolate the amplitude-frequency determining the temporally varying trend of NDVI, and spatial overlay analysis was used to analyze the influence of land use and land cover change on vegetation dynamics. The results showed: (1) the average NDVI values of all pixels in Yanchi County, which were composited annually by the MVC method, ranged from 0.2 to 0.4 in the period 2000-2012. The vegetation index in this area was very low because there is a typical desert steppe, but significantly (P < 0.05) increased by 0.078 per 10 a, which was faster than that in the Three-North Shelter Forest Program region. Overall, the vegetation in Yanchi County lacks stability and has frequent, large-amplitude inter-annual fluctuations. (2) The Empirical Mode Decomposition found that the NDVI time-series data included two Intrinsic Mode Function (IMF) components with 4 and 9 year quasi-periodic fluctuations. The variance contribution of the first IMF component was about 50%, almost the same as that of the NDVI residue component, which increased significantly over the 13 years. However, the intensity of NDVI fluctuation decreased because the fluctuation in precipitation, one of its main driving factors, declined. (3) Improvements in land use and land cover change were the main drivers for NDVI increase. The former made a larger contribution than the latter. Therefore, protection is the first option for improving the ecological environment, and proper reconstruction can be used as a supplement in desert steppe. A proper strategy for vegetation restoration and maintenance should be adopted, and overall protection can be implemented through scientific and harmonized development.