To achieve both water conservation and climate change mitigation benefits, photovoltaic water pumping (PVWP) system, which employs solar energy to fuel the water pumping system, has been a widely adopted solar energy technology in the last two decades. Although the PVWP system is driven by direct renewable flux, and has no onsite CO2 emissions, there must be energy consumed during the production of PV modules and the operation of water pumping system. Thus, we estimated the CO2 emissions of a PVWP system in Inner Mongolia, China in a life cycle perspective. A hybrid Life Cycle Analysis (LCA), which combines process-sum and economic input-out analysis was employed to reduce uncertainty. Results show that PVWP is a good choice for carbon emission reduction with carbon sequestration benefit much higher than the lifetime carbon emissions. The largest emitters are PV module and engineering, which should be the focus of carbon management of PVWP system.