Numerical weather simulations and forecasts are highly sensitive to environmental conditions. This is especially true in Taiwan, an ocean-surrounded island, during its transition season. Atmospheric temperature and moisture profiles retrieved from spaceborne sounders provide essential environmental information in regions lacking in situ observations. However, infrared sounders are sensitive to clouds and may induce uncertainties related to cloud properties. The present study analyzed 1 year of soundings from the National Oceanic and Atmospheric Administration’s Unique Combined Atmospheric Processing System (NUCAPS) to investigate the effects of clouds on the retrievals. The results indicated that the retrieved temperature profiles over land and under clouds had greater uncertainty than over oceans or in clear skies. In addition, the moisture profiles often exhibited a bias against cloud-top pressure. Therefore, this study proposed an objective quality control and bias correction method based on cloud effects. Excluding temperature observations affected by clouds and those over land reduced the root mean square difference from 3.3 K to 1.3 K. The relative cloud-top pressure level was used to conduct water vapor bias correction, which achieved effective correction for dry bias in the retrieved moisture profiles. After appropriate constraint criteria were applied, the bias-corrected profiles demonstrated a reduction in moisture bias from −4% to nearly 0%. That is, we assimilated sounding and radiance data into the regional Weather Research and Forecasting model and evaluated their effects, and we discovered that the retrieved profiles and direct observations positively contributed to the forecast of a spring frontal system. However, experiments using objective-bias-corrected sounding data improved skill scores in precipitation forecasts compared with using original sounding data or radiance data under a standard global operational baseline bias correction.