The dynamics of belowground net primary productivity (BNPP) is of fundamental importance in understanding carbon (C) allocation and storage in grasslands. However, our knowledge of the interannual variability in response of BNPP to ongoing global warming is limited. In this study, we explored temporal responses of BNPP and net primary productivity (NPP) partitioning to warming and clipping in a tallgrass prairie in Oklahoma, USA. Infrared heaters were used to elevate soil temperature by approximately 2 °C since November 1999. Annual clipping was to mimic hay harvest. On average from 2005 to 2009, warming increased BNPP by 41.89% in the unclipped subplots and 66.93% in the clipped subplots, with significant increase observed in wet years. Clipping also had significant positive impact on BNPP, which was mostly found under warming. Overall, fBNPP, the fraction of BNPP to NPP, increased under both warming and clipping treatments, more in dry years. Water availability (either precipitation or soil moisture) was the most limiting factor for both BNPP and fBNPP. It strongly dominated the interannual variability in NPP, fBNPP, and their responses to warming and clipping. Our results suggest that water availability regulates tallgrass prairie's responses to warming and land use change, which may eventually influence the global C cycle. With increasing variability in future precipitation patterns, warming effects on the vegetation in this region may become less predictable.