Radiance measurements from a geostationary hyperspectral infrared sounder (GeoHIS) with high temporal resolution not only provide a continuous weather cube of atmospheric temperature and moisture information at different pressure levels, but also enable derivation of three‐dimensional (3D) horizontal winds by tracking atmospheric water vapor features. However, GeoHIS radiances are influenced by sub‐footprint cloudiness, which needs to be considered in tracking the moisture features for deriving the atmospheric wind fields. By combining the collocated high spatial resolution cloud information from an imager onboard the same platform, the 3D horizontal wind retrievals can be improved, and the influence of sub‐footprint cloudiness on winds can be quantified for better applications. Using data from the Advanced Geostationary Radiation Imager (AGRI) and Geostationary Interferometric Infrared Sounder onboard the same experimental geostationary satellite Fengyun‐4A, it is found that 3D horizontal wind retrievals can be derived under both clear and partially clear skies with reasonable accuracy. Sub‐footprint cloud information provides noticeable improvement in wind retrievals; higher/lower clouds have more/less influence while thicker/thinner clouds have more/less influence, respectively, on the wind product. The sub‐footprint cloudiness (cloud‐top pressure and cloud coverage) provides a good indication of the quality flag for quantitative applications of the 3D horizontal wind product. Plain Language Summary: Radiance measurements from a geostationary hyperspectral infrared sounder (GeoHIS) with high temporal resolution not only provide a continuous weather cube of atmospheric temperature and moisture at different pressure levels, but also enable derivation of three‐dimensional (3D) horizontal winds from tracking atmospheric water vapor features. The World Meteorological Organization's vision on an integrated observing system in 2040 states the requirement for five GeoHIS for complete earth coverage. The associated new information allows quantitative applications of both thermodynamic and dynamic information. Understanding the influence of sounder sub‐footprint cloudiness on wind retrievals is very important to quantifying the uncertainties in this new information. Using the collocated high spatial, spectral, and temporal resolution cloud information from AGRI and Geostationary Interferometric Infrared Sounder onboard the same experimental geostationary satellite FengYun‐4A, 3D horizontal wind fields are derived under both clear and partially cloudy skies (note that vertical component of the wind vector is not derived here). It is found that sub‐footprint cloudiness has a substantial influence on wind retrievals that needs to be considered in quantitative applications. Placing a high spatial resolution imager and a hyperspectral infrared sounder on the same geostationary platform enables quantifying the sounder sub‐footprint cloudiness better and thus improves retrieval and application of the atmospheric 3D horizontal winds. Key Points: 3D horizontal winds can be derived from high temporal resolution geostationary hyperspectral infrared sounder (GeoHIS) radiance measurements under both clear and partially cloudy skiesIt is found that sub‐footprint cloudiness has a substantial influence on 3D horizontal wind retrievals, which needs to be considered in quantitative applicationsCollocated high spatial resolution cloud information from an onboard imager will help 3D horizontal wind retrievals from GeoHIS by better quantifying the sub‐footprint cloudiness [ABSTRACT FROM AUTHOR]