Grassland productivity in response to climate change and land use is a global concern. In order to explore the effects of climate change and land use on net primary productivity (NPP), NPP partitioning [fBNPP, defined as the fraction of belowground NPP (BNPP) to NPP], and rain-use efficiency (RUE) of NPP, we conducted a field experiment with warming (+3 °C), altered precipitation (double and half), and annual clipping in a mixed-grass prairie in Oklahoma, USA since July, 2009. Across the years, warming significantly increased BNPP, fBNPP, and RUEBNPP by an average of 11.6%, 2.8%, and 6.6%, respectively. This indicates that BNPP was more sensitive to warming than aboveground NPP (ANPP) since warming did not change ANPP and RUEANPP much. Double precipitation stimulated ANPP, BNPP, and NPP but suppressed RUEANPP, RUEBNPP, and RUENPP while half precipitation decreased ANPP, BNPP, and NPP but increased RUEANPP, RUEBNPP, and RUENPP. Clipping interacted with altered precipitation in impacting RUEANPP, RUEBNPP, and RUENPP, suggesting land use could confound the effects of precipitation changes on ecosystem processes. Soil moisture was found to be a main factor in regulating variation in ANPP, BNPP, and NPP while soil temperature was the dominant factor influencing fBNPP. These findings suggest that BNPP is critical point to future research. Additionally, results from single-factor manipulative experiments should be treated with caution due to the non-additive interactive effects of warming with altered precipitation and land use (clipping).