Reducing the uncertainties in carbon balance assessment is essential for better pastureland management in arid areas. Climate forcing data are some of the major uncertainty sources. In this study, a modified Biome-BGC grazing model was driven by an ensemble of reanalysis data of the Climate Forecast System Reanalysis data (CFSR), the European Centre for Medium-Range Weather Forecasts Interim Reanalysis (ERA-Interim), and the Modern-Era Retrospective Analysis for Research and Applications (MERRA), to study the effect of climate change and grazing on the net ecosystem exchange (NEE) of the pasturelands in Central Asia. Afterwards, we evaluated the performance of corresponding climate datasets over four major pastureland types, and quantified the modeling uncertainty induced by climate forcing data. Our results suggest that (1) a significant positive trend in temperature and a negative trend in precipitation were obtained from the three climate datasets. The average precipitation is apparently higher in the CFSR and MERRA data, showing the highest temperature value among the data sets; (2) pasturelands in Central Asia released 2.10 ± 1.60 Pg C in the past 36 years. The highest values were obtained with the CFSR (−1.53 Pg C) and the lowest with the MERRA (−2.35 Pg C) data set; (3) without grazing effects, pasturelands in Central Asia assimilated 0.13 ± 0.06 Pg C from 1981–2014. Grazing activities dominated carbon release (100%), whereas climate changes dominated carbon assimilation (offset 6.22% of all the carbon release). This study offered possible implications to the policy makers and local herdsmen of sustainable management of pastureland and the adaptation of climate change in Central Asia.