Atmospheric fronts embedded in extratropical cyclones are high-impact weather phenomena, contributing significantly to midlatitude winter precipitation. The three vital characteristics of the atmospheric fronts, high wind speeds, abrupt change in wind direction, and rapid translation, force the induced surface waves to be misaligned with winds exclusively behind the cold fronts. The effects of the misaligned waves on air-sea fluxes remain undocumented. Using the multi-year in situ near-surface observations and direct covariance flux measurements from the Pioneer Array off the coast of New England, we find that the majority of the passing cold fronts generate misaligned waves behind the cold front. Once generated, the waves remain misaligned, on average, for about 8 hours. The fully-coupled model simulations indicate that the misaligned waves significantly increase wave roughness length (300%), drag coefficient (30%), and momentum flux (20%). The increased surface drag reduces the wind speeds in the surface layer. The upward turbulent heat flux is weakly decreased by the misaligned waves because of the compensating effect between the decrease in temperature and humidity scaling parameters and the increase in friction velocity. The misaligned wave effect is not accurately represented in a commonly used wave-based bulk flux algorithm. Yet, the suggested modification to the current formulation improves the overall accuracy of parameterized momentum flux estimates. The results imply that better representing a directional wind-wave coupling in the bulk formula of the numerical models may help improve the air-sea interaction simulations under the passing atmospheric fronts in the midlatitudes.