The vertical transport of water vapor by a severe convective process occurring in Nagqu area over the Tibetan Plateau has been investigated using the Weather Research Forecast (WRF) model with different cloud microphysical schemes. The simulated characteristics of the storm reveal good agreement with observations, such as the onset and location of convection and precipitation. The results show that when the convective cloud arises, the upward flux of water vapor over the convective region increases at first then declines with altitude, and is not sensitive to cloud microphysical schemes. Similar trend is also found for the total water vapor integrated over a period of 24 hours. A further analysis shows that this trend is correlated to the vertical updraft in the cloud, that is, both the short-time humidifying effect in the upper troposphere and duration are sensitive to cloud microphysical parameterization schemes. The largest difference of the maximum upper tropospheric water vapor mixing ratio can reach 20.3% among different schemes, leading to humidifying lasting from 1.5 to 7 hours. Taking a 24-hour average can reduce the sensitivity of upper troposphere humidity, but the maximum still reaches 14.3%. The results of this study indicate that when the WRF model is used for studies of the effects of deep convection on the upper tropospheric water vapor, the uncertainty induced by using different microphysical schemes cannot be neglected within 24-hour time scale.