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Global warming threatens ecosystem functions, biodiversity, and rangeland productivity in Mongolia. The study analyzes the spatial and temporal distributions of the Net Primary Production (NPP) and its response to climatic parameters. The study also highlights how various land cover types respond to climatic fluctuations from 2003 to 2018. The Boreal Ecosystem Productivity Simulator (BEPS) model was used to simulate the rangeland NPP of the last 16 years. Satellite remote sensing data products were mainly used as input for the model, where ground-based and MODIS NPP were used to validate the model result. The results indicated that the BEPS model was moderately effective (R2 = 0.59, the Root Mean Square Error (RMSE) = 13.22 g C m−2) to estimate NPP for Mongolian rangelands (e.g., grassland and sparse vegetation). The validation results also showed good agreement between the BEPS and MODIS estimates for all vegetation types, including forest, shrubland, and wetland (R2 = 0.65). The annual total NPP of Mongolia showed a slight increment with an annual increase of 0.0007 Pg (0.68 g C per meter square) from 2003 to 2018 (p = 0.82) due to the changes in climatic parameters and land cover change. Likewise, high increments per unit area found in forest NPP, while decreased NPP trend was observed in the shrubland. In conclusion, among the three climatic parameters, temperature was the factor with the largest influence on NPP variations (r = 0.917) followed precipitation (r = 0.825), and net radiation (r = 0.787). Forest and wetland NPP had a low response to precipitation, while inter-annual NPP variation shows grassland, shrubland, and sparse vegetation were highly sensitive rangeland types to climate fluctuations.