Although the influences of desertification and nitrogen (N) addition in shaping species composition and community structure have long been explored, our understanding of the underlying processes is not yet strong. Analyses of trends in the turnover and nestedness components of beta diversity can be informative of the processes response to N addition and desertification in desert steppe ecosystems. Our investigation of the changes in beta diversity under desertification and N addition in a desert steppe ecosystem in northern China showed desertification to significantly decrease beta diversity among communities, which leads to species homogenization. Further, decreases to the turnover component of beta diversity was likely an important factor causing homogenization under desertification. Although nitrogen addition did not fundamentally influence beta diversity, dissimilarity caused by nestedness significantly increased with nitrogen addition. The contrasting effects of desertification and N addition on the turnover and nestedness components of beta diversity suggest that the ordered loss of plant species with desertification improvement. Overall, our findings provide strong evidence that the effects of desertification and N addition on beta diversity change with ecological processes. We recommend that conservation strategies that focus management practices on prevention of desertification will be most effective in maintaining species diversity.