Precipitable water vapor (PWV) is a crucial factor in regulating the Earth’s climate. Moreover, it demonstrates a robust correlation with precipitation. Situated in a region known for the generation and development of tropical cyclones, Guangxi in China is highly susceptible to floods triggered via intense rainfall. The atmospheric water vapor in this area displays prominent spatiotemporal features, thus posing challenges for precipitation forecasting. The water vapor products within the MERRA-2 and ERA5 reanalysis datasets present an opportunity to overcome constraints associated with low spatiotemporal resolution. In this study, the PWV data derived from GNSS and meteorological measurements in Guangxi from 2016 to 2018 were used to evaluate the accuracy of MERRA-2 and ERA5 water vapor products and their relationship with water vapor variations during extreme rainfall. Using GNSS PWV as a reference, the average bias of MERRA-2 PWV and ERA5 PWV for heavy rainfall was −0.22 mm and 1.84 mm, respectively, with average RMSE values of 3.72 mm and 3.31 mm. For severe rainfall, the average bias of MERRA-2 PWV and ERA5 PWV was −0.14 mm and 2.92 mm, respectively, with average RMSE values of 4.28 mm and 4.01 mm. During heavy rainfall days from Days 178 to 184 in 2017, the average bias of MERRA-2 PWV and ERA5 PWV was 0.92 mm and 2.42 mm, respectively, with average RMSE values of 4.04 mm and 3.40 mm. The accuracy was highest at the Guiping and Hechi stations and lowest at the Hezhou and Rongshui stations. Furthermore, when comparing MERRA-2/ERA5 PWV with GNSS PWV and actual precipitation, the trends in the variations of MERRA-2/ERA5 PWV were generally consistent with GNSS PWV and aligned with the increasing or decreasing trends of actual precipitation. In addition, ERA5 PWV exhibited high accuracy. Before the onset of heavy rainfall, PWV has a sharp surge. During heavy rainfall, PWV reaches its peak value. Subsequently, after the cessation of heavy rainfall, PWV tends to stabilize. Therefore, the reanalysis data of PWV can effectively reveal significant changes in water vapor and actual precipitation during periods of heavy rainfall in the Guangxi region.