Abstract: The hyperspectral data from the Geostationary Interferometric Infrared Sounder (GIIRS) of the new-generation geostationary meteorological satellite FY-4A can be used to detect three-dimensional structure of atmosphere temperature and humidity by means of infrared hyperspectral interference spectroscopy, and a breakthrough has been made in detecting the atmosphere in geostationary orbit. Precipitable water vapor (PWV) from ground-based Global Navigation Satellite System (GNSS) is an effective means for continuous monitoring of atmospheric water vapor. In order to improve the reliability of water vapor from FY-4A hyperspectral sounder data, the GNSS/PWV, the atmospheric water vapor profiles retrieved by FY-4A/GIIRS and conventional radiosonde data from June to August in 2018 are analyzed. The high-precision atmospheric water vapor data monitored by GNSS and the GNSS/PWV and FY-4A/GIIRS water vapor profiles are rapidly merged to improve the accuracy of satellite retrievals of atmospheric water vapor profile. The results show that compared with conventional radiosonde data, the RMSE of the real-time product for atmospheric profile retrievals of FY-4A/GIIRS is 4.5 g/kg in the lower atmosphere, 2.4 g/kg at 700 hPa, and less than 1.5 g/kg above 500 hPa due to less water vapor content. By merging GNSS/PWV and water vapor profiles of FY-4A/GIIRS, the root mean square error of the whole layer is reduced by about 20%, and the root mean square error from near the surface to 600 hPa is reduced by 20%—25%, especially between 850 hPa and 700 hPa. The merging method can greatly improve the availability of satellite retrieval data. Through the application analysis of a rainstorm process with multiple system effects, it is found that the merging of GNSS/PWV and FY-4A/GIIRS can obtain atmospheric water vapor profiles with high spatial and temporal resolutions, which play a very important role in the nowcast of heavy rainfall.