The changes of land-use and management practices have profound influences on ecosystem structure and functioning, such as carbon cycle, which may exaggerate climate change's impacts. The terrestrial ecosystem carbon cycle is an important part of the global carbon cycle. With vast area and huge soil carbon pool, grasslands play an important role in the global carbon balance process, which is often disturbed and destroyed by reclamation easily. The long-term unreasonable reclamation resulted in a significant loss of ecological functions such as ecosystem carbon exchange in the desert grassland in the Inner Mongolia. A large number of croplands were abandoned with the gradual implementation of Grain for Green Project, which led to the grassland ecological function be restored effectively by natural restoration succession. These croplands, which have huge area and carbon sink potential, have become the focus of carbon cycle research in desert grassland ecosystem. However, the clearer understanding of the effects of cropland abandonment and its time effects on the ecosystem CO2 exchange processes is still needed. In this study, the ecosystem CO2 exchange (net ecosystem CO2 exchange, NEE; gross ecosystem production, GEP; and ecosystem respiration, ER), water use efficiency (WUE), and vegetation biomass were measured in the undisturbed desert steppe and recovery steppe with succession stages of 6, 12 and 17 years. The results showed that the species richness of perennials was improved effectively with Grain for Green. Compared with the local native grassland, the aboveground biomass recovered to 74.2%, 75.9% and 94.4% in early stage of recovery (PR, 2013-2014), mid-term stage of recovery (MR, 2007-2008), and late stage of recovery (AR, 2002-2003) plots, respectively. The longer Grain for Green time also caused a strong increase in perennials biomass, and reducing in annuals biomass and annuals/perennials ratio. In humid years, as the time of succession restoration goes on, the ecosystem CO2 exchange shows a significant upward trend, and there has been no significant difference on NEE between the late succession and the undisturbed desert grassland. The change trend of the ecosystem WUE is basically consistent with the ecosystem CO2 exchange. However, the WUE in the returned grassland has not recovered to the level of undisturbed desert grassland even after 17 years of farmland conversion. These results may mainly relate to the succession changes of the vegetation biomass and the annuals/perennial ratio. The results also show that the restoration of ecosystem function is not simultaneous, but selective in desert grassland after abandoning cropland.