To know the vegetation changes in the southern Maowusu Desert, the vegetation dynamic in above area from 2000 to 2013 was analyzed from the Normalized Difference Vegetation Index (NDVI), based on the Moderate Resolution Imaging Spectroradiometer (MODIS). The results show that the annual averages of NDVI presented a rising tendency with an annual growth rate of 2.69×10-3/year. The changes of the spatial maximums of the annual averages of NDVI were insignificant, with an increasing trend. Using the transfer matrix method, the NDVI values were divided into different levels and the transfer matrix of vegetation index was built. The yearly transfers of the NDVI levels were further analyzed. Comparing the NDVI values and NDVI levels of this year to that of last year, the NDVI shows a trend of getting better generally. The vegetation levels of 72.37% of the pixels became better in 2013 compared with that in 2000. The numbers of NDVI values in different levels in the transfer matrix in 2013 compared with that in 2000 were analyzed and the result suggests that, the NDVI values moved from the lower to the upper triangular of the transfer matrix, and the numbers of pixels in the upper triangular were much larger than that in the lower. This result suggests that the NDVI presents a tendency of a transformation from the lower level to the higher, and the vegetation became better gradually. In the whole, the vegetation of the southern Maowusu Desert was getting better continuously from 2000 to 2013.