Species diversity and functional diversity are the hot issues in ecology. The research on the relationship between them is the key to understand the function and process of community ecosystem. Based on variance analysis and principal component analysis, the relationship between plant species diversity and functional diversity was studied by using the function fitting analysis. The results showed that: (1) The vegetation functional diversity of limestone soil increased significantly (P<0.05) compared with the free grazing conditions. With the increase of the enclosure period, species diversity decreased significantly (P<0.05). The functional diversity did not change significantly (P>0.05). The plant functional diversity and species diversity in the aeolian soil area did not change significantly (P>0.05). (2) The relationship between functional diversity and species richness could be described by a quadratic polynomial Y=aX²+bX+c. With the increase of the enclosure period, the correlation coefficient of the two factors increased in both habitats of limestone soil and aeolian soil. In conclusion, the species diversity was positively correlated with the functional diversity in desert steppe, showing aquadratic function relationship. The species diversity could be used to reflect the level of functional diversity of plant community, but the replacement effect was affected by the period of enclosure and grazing. With the increase of the enclosure period, the ability of species diversity to reflect functional diversity level increased. In the future, the multi-dimensional characteristics of diversity and different soil habitat types should be considered to maintain the relationship mechanism between diversity and ecosystem function.