High latitude air-sea interaction is an important component of the earth’s climate system and the exchanges of mass and energy over the sea ice zone are very complicated processes that are not well understood. In this paper, we perform a series of sensitivity experiments to examine the effect of sea ice concentration on the development of boundary layer roll clouds. The experiments are performed at a very high spatial resolution that can resolve the individual convective roll clouds therefore allowing for a more realistic representation of the dynamic and thermodynamic processes in a large domain so as to allow for the downstream development of the boundary layer and the roll clouds. The high spatial resolution of the experiments allows for an explicit representation of the heterogeneity within the sea ice zone. This work reveals some interesting characteristics that have not been addressed in the previous studies due to coarse resolution and/or limited domain size. The results show that the sea ice zone has a significant impact on the atmospheric boundary development, which can be seen in both the evolution of the atmospheric variables and the development of vertical heat and moisture transfer patterns. In particular, we find the exchange of momentum, moisture and heat fluxes are different due to the heterogeneity in sea ice concentration, which suggest more realistic representations of processes over the sea ice zone are needed to properly calculate the associated energy and mass exchange budgets in current climate models. We also find that both thermodynamical and dynamical instabilities play a role in modifying the convection pattern over the sea ice zone, where the buoyancy forcing quickly increases while the wind shear is gradually eroded.