The presence or absence of sea ice introduces a substantial perturbation to surface‒atmosphere energy exchanges. Comprehending the effect of varying sea ice cover on surface‒atmosphere interactions is an important consideration for understanding the Arctic climate system. The recurring North Water Polynya (NOW) serves as a natural laboratory for isolating cloud responses to a rapid, near-step perturbation in sea ice. In this study, we employed high-resolution Arctic System Reanalysis version 2 (ASRv2) data to estimate turbulent heat fluxes over the NOW and nearby sea ice (NSI) area between 2005/2006 and 2015/2016. The results indicate that the average turbulent heat fluxes in the polynya are about 87% and 86% higher than in the NSI area over the 10 years during the entire duration of the polynya and during polar night, respectively. Enhanced turbulent heat fluxes from the polynya tend to produce more low-level clouds. The relationship between the polynya and low cloud in winter was examined based on Cloud‒Aerosol Lidar and Infrared Pathfinder Satellite Observations (CALIPSO). The low-cloud fraction (0–2 km) was about 7–34% larger over the polynya than the NSI area, and the ice water content below 200 m was about 250%–413% higher over the former than the latter. The correlation between cloud fraction and turbulent heat fluxes in the polynya peaks around the altitude of 200–300 m. These results suggest that the NOW affects the Arctic boundary layer cloudiness and structure in wintertime. Furthermore, higher horizontal resolution reanalysis data can advance our understanding of the cloud-polynya response.